pCT - User contributions [en]

Cluster convolution for GATE

2019-04-01T11:56:02Z

Hpe090: Added code to take edep arguments

In her MSc project, Silje Grimstad made a filtered library of the clusters from the summer beamtest in Heidelberg.

The result is ~15k Helium clusters stored as x/y arrays in a [[:File:database_final.zip|ROOT file included here]].

{| class="wikitable"
|-
! x_mean
! y_mean
! size
! hit_array
! height
! width
! x_start
! y_start
! i_event
! combined
|-
| float
| float
| int
| list<int>
| int
| int
| int
| int
| int
| bool
|}

A random sample of 9 clusters is shown below:

[[File:9_clusters.png|600px]]

We want to convolute a GATE simulation with clusters from this library. For each hit in the MC data, we pick a random cluster from the library and draw it around the hit position.
To do this, use the code at the bottom, with the following result:

[[File:original_vs_convoluted_hitmap.PNG|1000px]]

Below is example code to perform the diffusion on-fly using a Hits container class with Hit objects (x,y,layer,edep,eventID).
For more information about the implementation see [https://github.com/HelgeEgil/focal GitHub].

<source lang="cpp">
#include <TTree.h>
#include <TFile.h>
#include <TRandom3.h>
#include <list>
#include <vector>

using namespace std;

void makeSortedClusterDatabase();
Hits * diffuseHits(TRandom3 * gRandom, Hits * singlePixelHits);

TTree * CDB_treeCluster;
list<Int_t> * CDB_hit_array = 0;
TBranch * CDB_b_hit_array;
TTreeIndex * CDB_index;
Int_t CDB_clusterSize;
Double_t CDB_x_mean, CDB_y_mean;
Int_t CDB_sortIndex[50];
TFile * CDB_fCluster;

void makeSortedClusterDatabase() {
// From GlobalConstants/MaterialConstants.C / .h

Int_t lastClusterSize = -1;
CDB_fCluster = new TFile("Data/ClusterSizes/ALPIDE/database_final.root", "READ");
CDB_treeCluster = (TTree*) CDB_fCluster->Get("database");
CDB_treeCluster->SetBranchAddress("size", &CDB_clusterSize);
CDB_treeCluster->SetBranchAddress("x_mean", &CDB_x_mean);
CDB_treeCluster->SetBranchAddress("y_mean", &CDB_y_mean);
CDB_treeCluster->SetBranchAddress("hit_array", &CDB_hit_array, &CDB_b_hit_array);

// Sort clusters based on cluster size
for (int i=0; i<50; i++) CDB_sortIndex[i] = -1;
CDB_treeCluster->BuildIndex("size");
CDB_index = (TTreeIndex*) CDB_treeCluster->GetTreeIndex();
for (int i=0; i<CDB_index->GetN()-1; i++) {
Long64_t local = CDB_treeCluster->LoadTree(CDB_index->GetIndex()[i]);
CDB_treeCluster->GetEntry(local);
if (lastClusterSize < 0 || lastClusterSize != CDB_clusterSize) {
CDB_sortIndex[CDB_clusterSize] = i;
lastClusterSize = CDB_clusterSize;
}
}
}

Hits * diffuseHits(TRandom3 *gRandom, Hits * singlePixelHits) {
// From HelperTools/getTracks.C

Int_t nHits = singlePixelHits->GetEntriesFast();
Hits * diffusedHits = new Hits();
Int_t x, y, outX, outY, layer, cs, eventID, idx_x, binPos;
Float_t edep;
Int_t randomClusterIdx;

for (Int_t h=0; h<nHits; h++) {
x = singlePixelHits->getX(h);
y = singlePixelHits->getY(h);
layer = singlePixelHits->getLayer(h);
edep = singlePixelHits->getEdep(h);
eventID = singlePixelHits->getEventID(h);

// The correspondence between CS and Edep [keV/um] is calculated from Ganesh's NIM A Proceedings article.
cs = 4.2267 * pow(edep, 0.6500) + 0.5;

// To keep any outliers within the tabulated clusters in the database
if (cs<2) cs=2;
if (cs>=27) cs=26;

randomClusterIdx = gRandom->Integer(CDB_sortIndex[cs+1] - CDB_sortIndex[cs]) + CDB_sortIndex[cs];
CDB_treeCluster->GetEntry(CDB_treeCluster->LoadTree(CDB_index->GetIndex()[randomClusterIdx]));

idx_x = 0;
Int_t thisCS = 0;
for (Int_t n : *CDB_hit_array) {
for (Int_t binPosPow = 0; binPosPow < 10; binPosPow++) {
binPos = pow(2, binPosPow);
if (binPos & n) {
outX = x + (idx_x - CDB_x_mean) + 0.5;
outY = y + (binPosPow - CDB_y_mean) + 0.5;
diffusedHits->appendPoint(outX, outY, layer, eventID, edep/CDB_clusterSize);
}
}
idx_x++;
}
}
return diffusedHits;
}

</source>

File:Database final.zip

2019-04-01T11:51:01Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

Documentation

2019-04-01T11:41:27Z

Hpe090: /* Software installation */

[[Main Page]] -> [[Documentation]]

== Mailing lists and collaborative tools ==
* Project web page: has to come
* General mailing list: pCT@uib.no
* [https://pctbergen.slack.com Slack project]

== Software installation ==
* [[Software tutorial at IFT]]
* [[ROOT installation]]
* [[Geant 4 installation]]
* [[Gate installation]]
* [[FLUKA installation]]
* [[Insight Toolkit (ITK) installation]]
*: https://itk.org/
*: https://github.com/InsightSoftwareConsortium/ITK
* [[Reconstruction Toolkit (RTK) installation]]
*: http://www.openrtk.org/
*: https://github.com/SimonRit/RTK
*[[DTC toolkit|DTC Toolkit for reconstruction]]
*: [[Software for design optimization|User guide and tutorial]]
*: https://github.com/HelgeEgil/focal (to be merged into gitlab)
*: [[Cluster convolution for GATE]]
* [[Visualization Toolkit (VTK) Installation and usage]]
*: http://www.vtk.org/
*: https://github.com/Kitware/VTK

== Software repository ==
We use the '''gitlab''' server hosted by IT of University of Bergen. We start with a repository per ''work package (wp)''. As there is overlap in terms of software, this structure might change in the future. Log in with your UiB account, then the administrators will give you access to the pCT group. If you don't have an account yet, get in contact with the group over the general [[Documentation#Mailing lists and collaborative tools | channels]]. There might be an admin mailing list later.

* [https://gitlab.uib.no/pct UiB gitlab web interface].

Further information:
* [https://docs.gitlab.com/ce/gitlab-basics/README.html Gitlab basics]
* [https://docs.gitlab.com/ee/workflow/README.html Gitlab workflow]

==== [[Gitlab best practice]] ====
==== [[Gitlab Developer FAQ]] ====
==== [[Gitlab Master FAQ]] ====

== Development workflow ==
Every logged-in user can access the main repository, however only a small group of administrators has write access. To contribute, a user creates a '''fork''' (see [[Documentation#Creating_a_project_fork | here]]) from the repository. This is a repository copy in the Gitlab system where a single developer or a group of developers have full access.

A local copy of the repository is required on the working machine in order to work on the project. This copy is referred to be a '''clone''' (see [[Documentation#Making_local_working_copy | here]]).

=== Default branch structure ===

The main repository has the following branches:
* '''production''': the latest production code, in this branch we have release tags
* '''master''': the latest stable release
* '''dev''': the development branch

In addition to those main branches there can be ''feature'' branches where development happens detached from the main branches. A ''feature'' branch is based on the ''dev'' branch and has a limited lifetime.

=== Creating a project fork ===
A ''project fork'' or ''repository fork'' is a copy of the original repository where a user or a group of users has/have full control. All development in our project is carried out in the individual forks. Branches of project forks are merged back into the main repository by '''merge requests''', preferably via '''fast forward''' merges. That requires developers to rebase project forks to the main repository and resolve all conflicts before requesting a merge.

[https://docs.gitlab.com/ce/gitlab-basics/fork-project.html How to fork a project]

Your repository fork is your sandbox, you can do whatever you want. Unless you have your own rules at hand right now you can apply the following:
* leave the ''master'' branch in sync with the main repository, do not make commits to it
* commit your changes to the ''dev'' branch
* if you start a new feature, and it's expected to take a while, make a ''feature'' branch, e.g. ''dev-feature'' and give the feature a name
* synchronize regularly to the main repository by rebasing (tutorial coming soon)

=== Making local working copy ===
A project is utilized through a local working copy referred to be a ''clone''. The project can be cloned from either the main repository in the group space or the fork in the user space depending on the role.

In the examples replace ''user'' and ''wpn'' (e.g. wp7) appropriately.

'''Note''': the gitlab offers two modes for the link to be cloned, you can choose ''ssh'' (default setting) or ''https''. If you can not clone with the proposed default link, try option ''https://''.

==== From the main repository ====
The main repository is cloned like
git clone https://gitlab.uib.no/pct/wpn.git

The upstream link can be changed later to any other repository like e.g. a development fork as follows (given the clone directory is the current working directory)
git remote set-url origin https://user@gitlab.uib.no/user/wpn.git

The originally cloned remote repository will get the identifier ''origin'' in your local clone.

==== From development fork ====
Clone directly from your development fork
git clone https://user@gitlab.uib.no/user/wpn.git

This will create a local directory ''wpn'', an optional argument after the link allows to change the directory name, e.g.
git clone https://user@gitlab.uib.no/user/wpn.git mywork

==== Multiple upstream repositories ====
As a more advanced option, multiple remote repositories can be added to the clone. All remote repositories are referenced through their identifiers, e.g. ''origin'' pointing to the fork and ''pctgroup'' pointing to main repository (chosen as an example).
git remote add pctgroup https://gitlab.uib.no/pct/wpn.git

==== Check configured upstream repositories ====
The configured upstream repositories can be checked with
git remote -v
This will display the identifier and link to the configured upstream repositories.

=== Pushing to development fork ===
Once you have added commits to e.g. the '''dev''' branch, those commits can be ''pushed'' upstream to the fork (if ''origin'' refers to the fork)
git push origin dev

Or using the direct link
git push https://user@gitlab.uib.no/user/wpn.git dev

=== Pull/Merge request ===
All updates to the main repository are made via ''merge requests'' (github refers to them as ''pull requests''). A merge request requires the code update to be in a mergable branch in a development fork.

Merge request are also used widely to share ''work-in-progress'' with your colleagues and for code reviews. Mark such Merge request with "'''WIP:'''".

==== Preparation ====
In order to avoid conflicts, first the fork has to be updated to the main repository. The idea behind this is that all potential conflicts can be resolved by the developer with the best knowledge about the matter, while the maintainer can simple merge ''fast-forward''.

This description expects ''origin'' pointing to the developers fork. All contributions are done to branch ''dev'', thus it must be updated with the latest version of branch ''dev'' of main repository.

# Fetch update from main repository
#: <pre> git fetch https://gitlab.uib.no/pct/wpn.git dev</pre>
#:* the update is now stored in the local index, we have fetched branch ''dev'' of the main repository
#:* check the log of this latest fetch
#: <pre> git log FETCH_HEAD</pre>
#:* FETCH_HEAD is a shorthand for the head of the last branch fetched and is valid only immediately after a fetch operation
# Rebase your development to the main repository, ''rebase'' means that all the new commits are done with respect to the tip of the specified branch. There can be ''merge conflicts'' which need to be resolved with appropriate changes and commits.
#: <pre> git rebase FETCH_HEAD dev</pre>
#:* keep in mind that FETCH_HEAD is only temporarily valid, so you should do this immediately after ''fetch'' (''log'' does not change anything)
#:* replace ''dev'' with appropriate branch name if other then ''dev'' is used; it is also possible to rebase a branch with other name to the remote branch, e.g.
#: <pre> git rebase FETCH_HEAD feature-name</pre>
# Check your commits and commit messages, eventually ''squash'' (combine) or ''reword''. This advanced option is described later.
# Push to fork. As the commit history has most likely been changed, the option ''-f'' (force) has to be used
#: <pre> git push -f origin dev </pre>

The branch ''dev'' in the fork is now ready for a merge request. The branch name can be adjusted, there is nothing preventing other branch names.

==== Example workflow for a Merge request ====
# Go to your gitlab user space at [https://gitlab.uib.no/user https://gitlab.uib.no/user] (replace ''user'' appropriately).
# Find the project fork, e.g. in the list of projects associated with you from the upper main menu.
# In the line with the many columns regarding the repository, click on the "+"-symbol on the right hand side and choose "New merge request"
# Select project and branch for both source and target, and click "Compare branches and continue". '''Remember''': in almost all cases you have to merge to branch ''dev'' or other feature branch, only in very rare cases to branch ''master''
# Review the list of commits in this merge request, give it a descriptive title and description, pick an assignee
# Submit the merge request

=== Importing an external package ===
The project will use a couple of external packages which are hosted in a different master repository. Copies of such external packages can be added to the gitlab server under our project group to provide a consistent package.

Here is a proposed workflow for importing a package which is already hosted in git.
# Create new repository in the pCT group or ask for creation, lets call it ''newPackage''
# Fork the repository to your user space
# Clone the package you want to import
#:<pre> git clone <some_external_link> newPackage # we give it the new name</pre>
#:<pre> cd newPackage</pre>
# Redirect upstream URL to the fork in your gitlab user space
#:<pre> git remote set-url origin https://user@gitlab.uib.no/user/newPackage.git</pre>
# Now make a forced push (option ''-f'') to import the repository to your fork
#:<pre> git push -f origin</pre>
# Create merge request to branch ''import'' (if not existing, ''master'' or any other appropriate branch) by following the instructions [[Documentation#Pull/Merge request | Pull/Merge request]]

== User documentation ==

Cluster convolution for GATE

2019-02-25T14:09:03Z

Hpe090:

In her MSc project, Silje Grimstad made a filtered library of the clusters from the summer beamtest in Heidelberg.
The result is ~15k Helium clusters stored as x/y arrays in a ROOT file:

{| class="wikitable"
|-
! x_mean
! y_mean
! size
! hit_array
! height
! width
! x_start
! y_start
! i_event
! combined
|-
| float
| float
| int
| list<int>
| int
| int
| int
| int
| int
| bool
|}

A random sample of 9 clusters is shown below:

[[File:9_clusters.png|600px]]

We want to convolute a GATE simulation with clusters from this library. For each hit in the MC data, we pick a random cluster from the library and draw it around the hit position.
To do this, use the code at the bottom, with the following result:

[[File:original_vs_convoluted_hitmap.PNG|1000px]]

The needed cluster database for this is located at [https://github.com/HelgeEgil/focal/blob/master/DTCToolkit/Data/ClusterSizes/ALPIDE/database_combined_clusters_filter.root GitHib].

<source lang="cpp">
#include <TTree.h>
#include <TFile.h>
#include <TRandom3.h>
#include <list>
#include <vector>

using namespace std;

void convert_root_file() {
TFile *fCluster = new TFile("database_combined_clusters_filter.root", "READ");
TFile *fSimulationIn = new TFile("simulationToBeClustered.root", "READ");
TFile *fSimulationOut = new TFile("simulationToBeClustered_clustered.root", "recreate");
TTree *treeCluster = (TTree*) fCluster->Get("database");
TTree *treeSimulationIn = (TTree*) fSimulationIn->Get("Hits");
TTree *treeSimulationOut = new TTree("Hits", "Clustered GATE tree");

Double_t x_mean, y_mean;
Int_t randomClusterIdx, binPos, idx_x;
list<Int_t> *hit_array = 0;
TBranch *b_hit_array;
TRandom3 *gRand = new TRandom3(0);
Float_t pixel_size = 0.02929;

Float_t x,y,z,outX, outY, outZ;
Int_t parentID, eventID, outEventID, outParentID, nClusters, timeInClockSpeed, PDGEncoding;

treeSimulationIn->SetBranchAddress("posX",&x);
treeSimulationIn->SetBranchAddress("posY",&y);
treeSimulationIn->SetBranchAddress("posZ",&z);
treeSimulationIn->SetBranchAddress("eventID",&eventID);
treeSimulationIn->SetBranchAddress("parentID",&parentID);
treeSimulationIn->SetBranchAddress("PDGEncoding", &PDGEncoding);

treeSimulationOut->Branch("posX", &outX, "posX/F");
treeSimulationOut->Branch("posY", &outY, "posY/F");
treeSimulationOut->Branch("posZ", &outZ, "posZ/F");
treeSimulationOut->Branch("eventID", &outEventID, "eventID/I");
treeSimulationOut->Branch("parentID", &outParentID, "parentID/I");
treeSimulationOut->Branch("clockTime", &timeInClockSpeed, "clockTime/I");

treeCluster->SetBranchAddress("x_mean", &x_mean);
treeCluster->SetBranchAddress("y_mean", &y_mean);
treeCluster->SetBranchAddress("hit_array", &hit_array, &b_hit_array);

nClusters = treeCluster->GetEntriesFast();
randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

for (Int_t i=0, N = treeSimulationIn->GetEntries(); i<N; ++i) {
treeSimulationIn->GetEntry(i);

timeInClockSpeed = 400 * eventID; // 10 us readout speed
outParentID = parentID; // =0 for a primary particle, >0 for secondaries
outEventID = eventID;
outZ = z;

randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

idx_x = 0;
if (abs(PDGEncoding) == 2212) { // Only apply this for protons
for (Int_t n : *hit_array) { // loop x
for (int binPosPow = 0; binPosPow < 10; binPosPow++) { // loop y
binPos = pow(2, binPosPow);
if (binPos & n) {
outX = x + (idx_x - x_mean) * pixel_size;
outY = y + (binPosPow - y_mean) * pixel_size;
treeSimulationOut->Fill();
}
}
idx_x++;
}
}
}

treeSimulationOut->Write();
}
</source>

Cluster convolution for GATE

2019-02-25T14:08:54Z

Hpe090:

In her MSc project, Silje Grimstad made a filtered library of the clusters from the summer beamtest in Heidelberg.
The result is ~15k Helium clusters stored as a x/y array in a ROOT file:

{| class="wikitable"
|-
! x_mean
! y_mean
! size
! hit_array
! height
! width
! x_start
! y_start
! i_event
! combined
|-
| float
| float
| int
| list<int>
| int
| int
| int
| int
| int
| bool
|}

A random sample of 9 clusters is shown below:

[[File:9_clusters.png|600px]]

We want to convolute a GATE simulation with clusters from this library. For each hit in the MC data, we pick a random cluster from the library and draw it around the hit position.
To do this, use the code at the bottom, with the following result:

[[File:original_vs_convoluted_hitmap.PNG|1000px]]

The needed cluster database for this is located at [https://github.com/HelgeEgil/focal/blob/master/DTCToolkit/Data/ClusterSizes/ALPIDE/database_combined_clusters_filter.root GitHib].

<source lang="cpp">
#include <TTree.h>
#include <TFile.h>
#include <TRandom3.h>
#include <list>
#include <vector>

using namespace std;

void convert_root_file() {
TFile *fCluster = new TFile("database_combined_clusters_filter.root", "READ");
TFile *fSimulationIn = new TFile("simulationToBeClustered.root", "READ");
TFile *fSimulationOut = new TFile("simulationToBeClustered_clustered.root", "recreate");
TTree *treeCluster = (TTree*) fCluster->Get("database");
TTree *treeSimulationIn = (TTree*) fSimulationIn->Get("Hits");
TTree *treeSimulationOut = new TTree("Hits", "Clustered GATE tree");

Double_t x_mean, y_mean;
Int_t randomClusterIdx, binPos, idx_x;
list<Int_t> *hit_array = 0;
TBranch *b_hit_array;
TRandom3 *gRand = new TRandom3(0);
Float_t pixel_size = 0.02929;

Float_t x,y,z,outX, outY, outZ;
Int_t parentID, eventID, outEventID, outParentID, nClusters, timeInClockSpeed, PDGEncoding;

treeSimulationIn->SetBranchAddress("posX",&x);
treeSimulationIn->SetBranchAddress("posY",&y);
treeSimulationIn->SetBranchAddress("posZ",&z);
treeSimulationIn->SetBranchAddress("eventID",&eventID);
treeSimulationIn->SetBranchAddress("parentID",&parentID);
treeSimulationIn->SetBranchAddress("PDGEncoding", &PDGEncoding);

treeSimulationOut->Branch("posX", &outX, "posX/F");
treeSimulationOut->Branch("posY", &outY, "posY/F");
treeSimulationOut->Branch("posZ", &outZ, "posZ/F");
treeSimulationOut->Branch("eventID", &outEventID, "eventID/I");
treeSimulationOut->Branch("parentID", &outParentID, "parentID/I");
treeSimulationOut->Branch("clockTime", &timeInClockSpeed, "clockTime/I");

treeCluster->SetBranchAddress("x_mean", &x_mean);
treeCluster->SetBranchAddress("y_mean", &y_mean);
treeCluster->SetBranchAddress("hit_array", &hit_array, &b_hit_array);

nClusters = treeCluster->GetEntriesFast();
randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

for (Int_t i=0, N = treeSimulationIn->GetEntries(); i<N; ++i) {
treeSimulationIn->GetEntry(i);

timeInClockSpeed = 400 * eventID; // 10 us readout speed
outParentID = parentID; // =0 for a primary particle, >0 for secondaries
outEventID = eventID;
outZ = z;

randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

idx_x = 0;
if (abs(PDGEncoding) == 2212) { // Only apply this for protons
for (Int_t n : *hit_array) { // loop x
for (int binPosPow = 0; binPosPow < 10; binPosPow++) { // loop y
binPos = pow(2, binPosPow);
if (binPos & n) {
outX = x + (idx_x - x_mean) * pixel_size;
outY = y + (binPosPow - y_mean) * pixel_size;
treeSimulationOut->Fill();
}
}
idx_x++;
}
}
}

treeSimulationOut->Write();
}
</source>

Cluster convolution for GATE

2019-02-25T14:05:28Z

Hpe090:

In her MSc project, Silje Grimstad made a filtered library of the clusters from the summer beamtest in Heidelberg.
The result is ~20k Helium clusters stored as a x/y array in a ROOT file:

{| class="wikitable"
|-
! x_mean
! y_mean
! size
! hit_array
! height
! width
! x_start
! y_start
! i_event
! combined
|-
| float
| float
| int
| list<int>
| int
| int
| int
| int
| int
| bool
|}

A random sample of 9 clusters is shown below:

[[File:9_clusters.png|600px]]

We want to convolute a GATE simulation with clusters from this library. For each hit in the MC data, we pick a random cluster from the library and draw it around the hit position.
To do this, use the code at the bottom, with the following result:

[[File:original_vs_convoluted_hitmap.PNG|1000px]]

The needed cluster database for this is located at [https://github.com/HelgeEgil/focal/blob/master/DTCToolkit/Data/ClusterSizes/ALPIDE/database_combined_clusters_filter.root GitHib].

<source lang="cpp">
#include <TTree.h>
#include <TFile.h>
#include <TRandom3.h>
#include <list>
#include <vector>

using namespace std;

void convert_root_file() {
TFile *fCluster = new TFile("database_combined_clusters_filter.root", "READ");
TFile *fSimulationIn = new TFile("simulationToBeClustered.root", "READ");
TFile *fSimulationOut = new TFile("simulationToBeClustered_clustered.root", "recreate");
TTree *treeCluster = (TTree*) fCluster->Get("database");
TTree *treeSimulationIn = (TTree*) fSimulationIn->Get("Hits");
TTree *treeSimulationOut = new TTree("Hits", "Clustered GATE tree");

Double_t x_mean, y_mean;
Int_t randomClusterIdx, binPos, idx_x;
list<Int_t> *hit_array = 0;
TBranch *b_hit_array;
TRandom3 *gRand = new TRandom3(0);
Float_t pixel_size = 0.02929;

Float_t x,y,z,outX, outY, outZ;
Int_t parentID, eventID, outEventID, outParentID, nClusters, timeInClockSpeed, PDGEncoding;

treeSimulationIn->SetBranchAddress("posX",&x);
treeSimulationIn->SetBranchAddress("posY",&y);
treeSimulationIn->SetBranchAddress("posZ",&z);
treeSimulationIn->SetBranchAddress("eventID",&eventID);
treeSimulationIn->SetBranchAddress("parentID",&parentID);
treeSimulationIn->SetBranchAddress("PDGEncoding", &PDGEncoding);

treeSimulationOut->Branch("posX", &outX, "posX/F");
treeSimulationOut->Branch("posY", &outY, "posY/F");
treeSimulationOut->Branch("posZ", &outZ, "posZ/F");
treeSimulationOut->Branch("eventID", &outEventID, "eventID/I");
treeSimulationOut->Branch("parentID", &outParentID, "parentID/I");
treeSimulationOut->Branch("clockTime", &timeInClockSpeed, "clockTime/I");

treeCluster->SetBranchAddress("x_mean", &x_mean);
treeCluster->SetBranchAddress("y_mean", &y_mean);
treeCluster->SetBranchAddress("hit_array", &hit_array, &b_hit_array);

nClusters = treeCluster->GetEntriesFast();
randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

for (Int_t i=0, N = treeSimulationIn->GetEntries(); i<N; ++i) {
treeSimulationIn->GetEntry(i);

timeInClockSpeed = 400 * eventID; // 10 us readout speed
outParentID = parentID; // =0 for a primary particle, >0 for secondaries
outEventID = eventID;
outZ = z;

randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

idx_x = 0;
if (abs(PDGEncoding) == 2212) { // Only apply this for protons
for (Int_t n : *hit_array) { // loop x
for (int binPosPow = 0; binPosPow < 10; binPosPow++) { // loop y
binPos = pow(2, binPosPow);
if (binPos & n) {
outX = x + (idx_x - x_mean) * pixel_size;
outY = y + (binPosPow - y_mean) * pixel_size;
treeSimulationOut->Fill();
}
}
idx_x++;
}
}
}

treeSimulationOut->Write();
}
</source>

Cluster convolution for GATE

2019-02-25T14:03:02Z

Hpe090: Made page

In her MSc project, Silje Grimstad made a filtered library of the clusters from the summer beamtest in Heidelberg.
The result is ~20k Helium clusters stored as a x/y array in a ROOT file:

{| class="wikitable"
|-
! x_mean
! y_mean
! size
! hit_array
! height
! width
! x_start
! y_start
! i_event
! combined
|-
| float
| float
| int
| list<int>
| int
| int
| int
| int
| int
| bool
|}

A random sample of 9 clusters is shown below:

[[File:9_clusters.png|600px]]

We want to convolute a GATE simulation with clusters from this library. For each hit in the MC data, we pick a random cluster from the library and draw it around the hit position.
To do this, use the code at the bottom, with the following result:

[[File:original_vs_convoluted_hitmap.PNG|1000px]]

The needed cluster database for this is located at [https://github.com/HelgeEgil/focal/blob/master/DTCToolkit/Data/ClusterSizes/ALPIDE/database_combined_clusters_filter.root GitHib].

<source lang="cpp">
#include <TTree.h>
#include <TFile.h>
#include <TRandom.h>
#include <list>
#include <vector>

using namespace std;

void convert_root_file() {
TFile *fCluster = new TFile("database_combined_clusters_filter.root", "READ");
TFile *fSimulationIn = new TFile("simulationToBeClustered.root", "READ");
TFile *fSimulationOut = new TFile("simulationToBeClustered_clustered.root", "recreate");
TTree *treeCluster = (TTree*) fCluster->Get("database");
TTree *treeSimulationIn = (TTree*) fSimulationIn->Get("Hits");
TTree *treeSimulationOut = new TTree("Hits", "Clustered GATE tree");

Double_t x_mean, y_mean;
Int_t randomClusterIdx, binPos, idx_x;
list<Int_t> *hit_array = 0;
TBranch *b_hit_array;
TRandom3 *gRand = new TRandom3(0);
Float_t pixel_size = 0.02929;

Float_t allZ = 0;
Int_t fillN = 0;
Float_t x,y,z,edep,outX, outY, outZ;
Int_t parentID, eventID, outEventID, outParentID, nClusters, timeInClockSpeed, PDGEncoding;
Char_t processName[17];

TCanvas *c = new TCanvas();
TH2C *hOrig = new TH2C("hOrig", "Original hitmap",1024,-15,15,512,-7.5,7.5);
TH2C *hNew = new TH2C("hNew", "New hitmap", 1024,-15,15,512,-7.5,7.5);
Int_t palette[2] = {kWhite, kBlack};

c->Divide(2,1);
gStyle->SetPalette(2, palette);

treeSimulationIn->SetBranchAddress("posX",&x);
treeSimulationIn->SetBranchAddress("posY",&y);
treeSimulationIn->SetBranchAddress("posZ",&z);
treeSimulationIn->SetBranchAddress("edep",&edep);
treeSimulationIn->SetBranchAddress("eventID",&eventID);
treeSimulationIn->SetBranchAddress("parentID",&parentID);
treeSimulationIn->SetBranchAddress("PDGEncoding", &PDGEncoding);

treeSimulationOut->Branch("posX", &outX, "posX/F");
treeSimulationOut->Branch("posY", &outY, "posY/F");
treeSimulationOut->Branch("posZ", &outZ, "posZ/F");
treeSimulationOut->Branch("eventID", &outEventID, "eventID/I");
treeSimulationOut->Branch("parentID", &outParentID, "parentID/I");
treeSimulationOut->Branch("clockTime", &timeInClockSpeed, "clockTime/I");

treeCluster->SetBranchAddress("x_mean", &x_mean);
treeCluster->SetBranchAddress("y_mean", &y_mean);
treeCluster->SetBranchAddress("hit_array", &hit_array, &b_hit_array);

nClusters = treeCluster->GetEntriesFast();
randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

for (Int_t i=0, N = treeSimulationIn->GetEntries(); i<N; ++i) {
treeSimulationIn->GetEntry(i);

timeInClockSpeed = 400 * eventID;
outParentID = parentID;
outEventID = eventID;
outZ = z;

if (z<2) hOrig->Fill(x,y);

randomClusterIdx = gRand->Integer(nClusters);
treeCluster->GetEntry(randomClusterIdx);

idx_x = 0;
if (abs(PDGEncoding) == 2212) {
for (Int_t n : *hit_array) { // loop x
for (int binPosPow = 0; binPosPow < 10; binPosPow++) { // loop y
binPos = pow(2, binPosPow);
if (binPos & n) {
outX = x + (idx_x - x_mean) * pixel_size;
outY = y + (binPosPow - y_mean) * pixel_size;
treeSimulationOut->Fill();
if (z<2) hNew->Fill(outX, outY);
}
}
idx_x++;
}
}
}

treeSimulationOut->Write();

c->cd(1);
hOrig->Draw("COL");
c->cd(2);
hNew->Draw("COL");

/*
delete fSimulationIn;
delete fSimulationOut;
delete fCluster;
*/
}
</source>

File:Original vs convoluted hitmap.PNG

2019-02-25T13:46:17Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

File:9 clusters.png

2019-02-25T13:44:20Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

Workpackages

2019-02-25T13:39:30Z

Hpe090: /* WP1: Physics simulation, verification and design optimization */

ASK link to people responsible for package / sub package?

== [[WP1]]: Physics simulation, verification and design optimization ==
* Beam scenarios – beam spot, intensity
* Detector specifications: [[DTC optimization|Optimization of geometry and segmentation]]
* Radiation environment - location
* Evaluation of rates (average/worst case) of the digital backend of the sensor
* Beam tests of sensors
* [[WP1 Ideas for project to pursue]]
* [[Cluster convolution for GATE]]

== [[WP2]]: Chip submission and sensor characterization ==
* Improved sensor and data encoding design
* Chip submission
* Testing of prototypes

== [[WP3]]: Data readout ==
* Optimisation of the readout electronics architecture
* SystemC simulation of rates (average/worst case) of the readout chain
* Development and testing of readout electronics
* Setting up a full readout chain
* Development of firmware and software

== [[WP4]]: Online systems ==
* Hardware infrastructure
* Software infrastructure
* DAQ software
* DCS + Trigger
* Data quality monitoring

== [[WP5]]: Assembly and System integration ==
* Assembly of chips into HICs/staves
* Assembly of staves into layers
* Integration of layers into a compact detector
* Mechanical and electrical integration, cooling
* Electronics and DAQ integration

== [[WP6]]: Commissioning ==
* Commissioning of the PRM in beams
* Performance evaluation in a pre-clinical environment, i.e. with phantoms

== [[WP7]]: Reconstruction software ==
* Calorimeter response
* Calorimeter track reconstruction
* Reconstruction of 3D trajectory – track vector matching
* 3D stopping power map

Main Page

2019-01-02T08:29:52Z

Hpe090: /* Workpackage Reports */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations) --- See also submitted article on design optimization
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* Daniel Aadnevik - MSc - 2014 - Extremely high-granularity digital tracking calorimeter for the detection of scattered protons in pCT
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [http://bora.uib.no/handle/1956/17757 Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]
* [http://bora.uib.no/handle/1956/18748 Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics). ]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).

==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Work in Progress ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:28:53Z

Hpe090: /* Under construction */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* Daniel Aadnevik - MSc - 2014 - Extremely high-granularity digital tracking calorimeter for the detection of scattered protons in pCT
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [http://bora.uib.no/handle/1956/17757 Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]
* [http://bora.uib.no/handle/1956/18748 Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics). ]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).

==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Work in Progress ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:28:16Z

Hpe090: /* In review */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* Daniel Aadnevik - MSc - 2014 - Extremely high-granularity digital tracking calorimeter for the detection of scattered protons in pCT
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [http://bora.uib.no/handle/1956/17757 Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]
* [http://bora.uib.no/handle/1956/18748 Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics). ]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).

==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:28:10Z

Hpe090: /* Journal Articles */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* Daniel Aadnevik - MSc - 2014 - Extremely high-granularity digital tracking calorimeter for the detection of scattered protons in pCT
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [http://bora.uib.no/handle/1956/17757 Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]
* [http://bora.uib.no/handle/1956/18748 Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics). ]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).

==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:27:30Z

Hpe090: /* Theses */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* Daniel Aadnevik - MSc - 2014 - Extremely high-granularity digital tracking calorimeter for the detection of scattered protons in pCT
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [http://bora.uib.no/handle/1956/17757 Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]
* [http://bora.uib.no/handle/1956/18748 Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics). ]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc (HVL) - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Alba Garcia Santos - MSc (Utrecht) - 2019 - Improvements of track reconstruction algorithms in pixel-based pCT calorimeters
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).

==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:25:56Z

Hpe090: /* Theses */ added MScs

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* Daniel Aadnevik - MSc - 2014 - Extremely high-granularity digital tracking calorimeter for the detection of scattered protons in pCT
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [http://bora.uib.no/handle/1956/17757 Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]
* [http://bora.uib.no/handle/1956/18748 Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics). ]
* [http://bora.uib.no/handle/1956/18058 Viljar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).]
* [http://bora.uib.no/handle/1956/18057 Susmita Afroz - MSc - 2018 - Noise and Cluster Size Studies of ALPIDE-CMOS Pixel Sensor for pCT]
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).

==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:19:20Z

Hpe090: /* Journal Articles */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. Kreftbehandling Med Protonterapi Og Proton CT. Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]
** [http://norskfysisk.no/filer/FFV/2017/FFV-2017-4.pdf Magazine at norskfysisk.no]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:17:25Z

Hpe090: /* Under construction */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. “Kreftbehandling Med Protonterapi Og Proton CT.” Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Rejected by Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:16:53Z

Hpe090: /* In review */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. “Kreftbehandling Med Protonterapi Og Proton CT.” Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]

==== In review ====
* Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
** Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

* Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

* Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography. Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
** Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Submitted to Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:14:14Z

Hpe090: /* Under construction */

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. “Kreftbehandling Med Protonterapi Og Proton CT.” Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]

==== In review ====
Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography.
* Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
* Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,.
* Submitted to Physics in Medicine and Biology.
* Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography.
* Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
* Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Submitted to Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2019-01-02T08:13:59Z

Hpe090: /* In review */ Added article

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. “Kreftbehandling Med Protonterapi Og Proton CT.” Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]

==== In review ====
Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography.
* Revision submitted to Web of Conferences after the "Connecting the Dots" conference.
* Revised manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,.
* Submitted to Physics in Medicine and Biology.
* Submitted manuscript: [[Media: Authors manuscript.pdf | PDF]]

Pettersen, Helge Egil Seime, Johan Alme, Gergely Gabor Barnafoldi, Alba Garcıa-Santos, Ola Grøttvik, Håvard Helstrup, Kristin Fanebust Hetland, Ilker Meric, Odd Harald Odland, Gabor Papp, Thomas Peitzmann, Dieter Röhrich, Joao Seco, Hesam Shafiee, Eivind Vågslid Skjæveland, Ganesh Tambave, Kjetil Ullaland, Monika Varga-Kofarago, Lennart Volz, Boris Wagner and Shiming Yang. Design Optimization of a Pixel Based Range Telescope for Proton Computed Tomography.
* Submitted to Physica Medica Special Issue: Advances in Geant4 for medicine.
* Submitted manuscript: [[Media: Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf| PDF]]

==== Under construction ====
* H. E. S. Pettersen, J. Sølie, I. Meric, D. Röhrich, O. H. Odland, etc.: Design optimization of a digital tracking calorimeter
** Preliminary manuscript: [[Media: Design optimization of a digital tracking calorimeter.pdf | PDF]]
** This paper might be generalized somewhat for publication

* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Submitted to Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

File:Pettersen et al. - Design Optimization of a Pixel Based Range Telesco.pdf

2019-01-02T08:12:24Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

Main Page

2018-12-06T15:33:07Z

Hpe090: /* Journal Articles */ Added Fra Fysikkens Verden

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

* Pettersen, H. E. S., and D. Röhrich. 2017. “Kreftbehandling Med Protonterapi Og Proton CT.” Fra Fysikkens Verden, December 2017.
** Published article: [[Media: FFV-proton-CT-ensidig.pdf | PDF]]

==== In review ====
Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Submitted to Web of Conferences after the "Connecting the Dots" conference.
** Proffered manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Proffered manuscript: [[Media: Authors manuscript.pdf | PDF]]

==== Under construction ====
* H. E. S. Pettersen, J. Sølie, I. Meric, D. Röhrich, O. H. Odland, etc.: Design optimization of a digital tracking calorimeter
** Preliminary manuscript: [[Media: Design optimization of a digital tracking calorimeter.pdf | PDF]]
** This paper might be generalized somewhat for publication

* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Submitted to Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

File:FFV-proton-CT-ensidig.pdf

2018-12-06T15:32:46Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

Main Page

2018-12-06T15:32:04Z

Hpe090: Added submitted publication

'''Wiki for the proton CT project'''

== [[Documentation]] ==
[[Documentation]] on how to install and use the involved software packages, the development workflow, etc.

== [[Publications]] ==
List of publications from the project.

==== Workpackage Reports ====
* [[Media:pCT-WP1-1-Rev2 design recommendations.pdf | pCT-WP1-01-Rev2 Detector design specifications]] (Rev2: Added carrier board thickness recommendations)
* [[:File:pCT-WP1-02-Rev3 (Radiation environment and electronics).pdf | pCT-WP1-02-Rev3 Radiation environment and placement of electronics]] (Rev2: Updated results and assumptions, Rev3: Updated with 1-10cm results) (Please feel free to contact [mailto:jars@hvl.no Jarle Rambo Sølie] if there are any questions regarding the contents of this document.

==== Theses ====
* [http://bora.uib.no/bitstream/handle/1956/10412/135279255.pdf?sequence=1&isAllowed=y Kristian Austreim - MSc - 2015 - Proton computed tomography readout testing and detector design]
* [http://bora.uib.no/bitstream/handle/1956/16041/thesis_final.pdf?sequence=1&isAllowed=y Ola Grøttvik - MSc - 2017 - Design of High-Speed Digital Readout System for Use in Proton Computed Tomography]
* [http://bora.uib.no/bitstream/handle/1956/16758/PCT_readout_testing_and_detector_HSchaug.pdf?sequence=1&isAllowed=y Håkon Schaug - MSc - 2017 - Proton Beam Test Of A High Granularity Calorimeter For Proton Computed Tomography]
* [https://brage.bibsys.no/xmlui/bitstream/handle/11250/2434108/16246_FULLTEXT.pdf?sequence=1&isAllowed=y Even Hansen - MSc - 2017 - Charge Diffusion Modelling for a Monolithic Active Pixel Sensor Detector with Application to Proton CT]
* [[:File:A digital tracking calorimeter for proton computed tomography.pdf | Helge Pettersen - PhD - 2018 - A Digital Tracking Calorimeter for Proton Computed Tomography]]
* Simon Kristian Huiberts - MSc - 2018 - Characterization of the ALPIDE chip using He ions (Data from Australian Micro beam, cluster size characteristics).
* Villiar Nilsen Ekeland - MSc - 2018 - Characterization of the ALPIDE chip using protons (Data from Oslo beam test, cluster size and LET correlation with different bias voltages).
* Silje Grimstad - MSc - 2019 - ALPIDE Cluster simulations (Building database of cluster characteristics, simulation of clusters using said database. Position and cluster separation algorithms).
* Aleksei Kuleshov - MSc - 2019 - Proton CT monitoring and ALPIDE control (MQTT protocol server, System workflow, GUI implementation).
==== Journal Articles ====
* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research A 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D. Accuracy of parameterized proton range models; a comparison. Radiation Physics and Chemistry, 144 (C): 295-297 (2018). doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

==== In review ====
Pettersen, H.E.S., Meric, I., Odland, O.H., Shafiee, H., Sølie, J., Röhrich, D. Proton Tracking Algorithm for Pixel Based Range Telescopes for Proton Computed Tomography. Submitted to Web of Conferences after the "Connecting the Dots" conference.
** Proffered manuscript: [[Media: detector-proton-tracking.pdf | PDF]]

Pettersen, Helge Egil Seime, Lennart Volz, Jarle Sølie, Dieter Rohrich, and Joao Seco. A Linear Projection Model to Estimate a Proton’s Position in a Pencil Beam For Single Sided Proton Imaging,. Submitted to Physics in Medicine and Biology.
** Proffered manuscript: [[Media: Authors manuscript.pdf | PDF]]

==== Under construction ====
* H. E. S. Pettersen, J. Sølie, I. Meric, D. Röhrich, O. H. Odland, etc.: Design optimization of a digital tracking calorimeter
** Preliminary manuscript: [[Media: Design optimization of a digital tracking calorimeter.pdf | PDF]]
** This paper might be generalized somewhat for publication

* J. Sølie, H. E. S. Pettersen, I. Meric, O. H. Odland, H. Helstrup and D. Röhrich: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations. Submitted to Radiat. Phys. Chem. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.
** Preliminary manuscript: [[Media: 1708.00668.pdf |PDF]]
** arXiv link: [https://arxiv.org/abs/1708.00668 arXiv:1708.00668]

== [[Meetings]] ==
Notes and slides from the project meetings

== [[Workshops]] ==
Slides from the project [[Workshops | workshops]]

== [[Workpackages]] ==
Sections for the different work packages

== [[People]] ==
Contact info of involved people

== [[Links]] ==
Link collection of topics regarding the project

== Getting started ==
* Note: ASK is a placeholder that marks questions
* Note: Search function is not ideal. It doesn't find all occurences of the search term, e.g. aries finds libraries but not aries.bccs

* Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

File:Authors manuscript.pdf

2018-12-06T15:31:27Z

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File uploaded with MsUpload

Main Page

2018-08-01T08:39:00Z

Hpe090: Added WoC paper

File:Detector-proton-tracking.pdf

2018-08-01T08:38:27Z

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File:A digital tracking calorimeter for proton computed tomography.pdf

2018-06-04T08:04:33Z

Hpe090: Hpe090 uploaded a new version of File:A digital tracking calorimeter for proton computed tomography.pdf

File uploaded with MsUpload

Publications

2018-06-04T08:01:17Z

Hpe090: /* From Bergen Proton CT group */

== From Bergen Proton CT group ==

==== Published ====

* Pettersen, H.E.S., J. Alme, A. van den Brink, M. Chaar, D. Fehlker, I. Meric, O.H. Odland, et al. Proton Tracking in a High-Granularity Digital Tracking Calorimeter for Proton CT Purposes. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 860C, 51–61. doi:10.1016/j.nima.2017.02.007.
** Published manuscript: [[Media: 1-s2.0-S0168900217301882-main.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0168900217301882 doi:10.1016/j.nima.2017.02.007]
** arXiv link: [https://arxiv.org/abs/1611.02031 arXiv:1611.02031]

* Pettersen, H.E.S., Chaar, M., Meric, I., Odland, O.H., Sølie, J., Röhrich, D., n.d. Accuracy of parameterized proton range models; a comparison. doi:10.1016/j.radphyschem.2017.08.02
** Published manuscript: [[Media: Comparison of different calculation methods of proton ranges.pdf | PDF]]
** Elsevier link: [http://www.sciencedirect.com/science/article/pii/S0969806X17303869?via%3Dihub 10.1016/j.radphyschem.2017.08.028]
** arXiv link: [https://arxiv.org/abs/1704.08854 arXiv:1704.08854]

==== In review ====

* J. Sølie, I. Meric and H. Pettersen: A comparison of longitudinal and lateral range for protons traversing complex media using GATE, MCNP6 and FLUKA Monte Carlo simulations.
** Preliminary manuscript: [[Media: NACP2017ActaDraft_(1).pdf |PDF]]
** Submitted to Rad. Chem. Phys. in conjunction with the [http://conferences.illinois.edu/irrma2017/ IRRMA X] conference.

==== Under construction ====

* H. Pettersen, J. Sølie, I. Meric, D. Röhrich, O. H. Odland, etc.: Design optimization of a pixelated proton range telescope
** Preliminary manuscript: [[Media: Design optimization of a digital tracking calorimeter.pdf | PDF]]
** This paper might be generalized somewhat for publication

* H. Pettersen, I. Meric, O. H. Odland, H. Shafiee, J. Sølie, D. Röhrich: Reconstruction of Proton Tracks Inside a Digital Tracking Calorimeter for Proton Computed Tomography
** To be submitted as part of the ''Connecting the Dots'' workshop proceedings, with deadline 2018-06-30.

== Review articles on proton CT ==
* G. Poludniowski, N.M. Allinson, P.M. Evans, '''Proton radiography and tomography with application to proton therapy''', The British Journal of Radiology. 88 (2015) 20150134. doi:10.1259/bjr.20150134.
* C. Civinini, '''Tracking for pCT - global status update''', (2013).

== Historical ==
* K.M. Hanson, C.A. Taylor, M.A. Paciotti, R.J. Macek, D.B. Laubacher, R.L. Hutson, T.M. Cannon, J.N. Bradbury, '''Computed tomography using proton energy loss''', Physics in Medicine and Biology. 26 (1981) 965.
* M. Urie, M. Goitein, W.R. Holley, G.T. Chen, '''Degradation of the Bragg peak due to inhomogeneities''', Physics in Medicine and Biology. 31 (1986) 1.
* K.M. Hanson, J.N. Bradbury, R.A. Koeppe, R.J. Macek, D.R. Machen, R. Morgado, M.A. Paciotti, S.A. Sandford, V.W. Steward, '''Proton computed tomography of human specimens''', Physics in Medicine and Biology. 27 (1982) 25.
* A.M. Koehler, '''Proton Radiography''', Science. 160 (1968) 303–304.
* M. Gotein, '''The measurement of tissue heterodensity to guide charged particle radiotherapy''', International Journal of Radiation Oncology Biological Physics. 3 (1977) 27–33.
* B. Schaffner, E. Pedroni, '''The precision of proton range calculations in proton radiotherapy treatment planning: experimental verification of the relation between CT-HU and proton stopping power''', Physics in Medicine and Biology. 43 (1998) 1579.
* H.F.-W. Sadrozinski, V. Bashkirov, B. Keeney, L.R. Johnson, S.G. Peggs, G. Ross, T. Satogata, R.W.M. Schulte, A. Seiden, K. Shanazi, D.C. Williams, '''Toward Proton Computed Tomography''', IEEE Transactions on Nuclear Science. 51 (2004) 3–9. doi:10.1109/TNS.2003.823044.

== On proton CT reconstruction with some novel approaches ==
* R. Rescigno, C. Bopp, M. Rousseau, D. Brasse, '''A pencil beam approach to proton computed tomography''', Medical Physics. 42 (2015) 6610–6624. doi:10.1118/1.4933422.
* C.T. Quiñones, J.M. Létang, S. Rit, '''Filtered back-projection reconstruction for attenuation proton CT along most likely paths, Physics in Medicine and Biology.''' 61 (2016) 3258–3278. doi:10.1088/0031-9155/61/9/3258.
* C. Bopp, J. Colin, D. Cussol, C. Finck, M. Labalme, M. Rousseau, D. Brasse, '''Proton computed tomography from multiple physics processes''', Physics in Medicine and Biology. 58 (2013) 7261–7276. doi:10.1088/0031-9155/58/20/7261.
* M. Bruzzi, N. Blumenkrantz, J. Feldt, J. Heimann, H.F.-W. Sadrozinski, A. Seiden, D.C. Williams, V. Bashkirov, R. Schulte, D. Menichelli, M. Scaringella, G.A.P. Cirrone, G. Cuttone, N. Randazzo, V. Sipala, D. Lo Presti, '''Prototype Tracking Studies for Proton CT''', IEEE Transactions on Nuclear Science. 54 (2007) 140–145. doi:10.1109/TNS.2006.889642.
* C. Bopp, R. Rescigno, M. Rousseau, D. Brasse, '''Quantitative proton imaging from multiple physics processes: a proof of concept''', Physics in Medicine and Biology. 60 (2015) 5325–5341. doi:10.1088/0031-9155/60/13/5325.
* C. Bopp, R. Rescigno, M. Rousseau, D. Brasse, '''The impact of tracking system properties on the most likely path estimation in proton CT''', Physics in Medicine and Biology. 59 (2014) N197–N210. doi:10.1088/0031-9155/59/23/N197.

== Publications on proton CT sorted by group ==

=== From PRaVDA ===
* M. Esposito, T. Anaxagoras, P.M. Evans, S. Green, S. Manolopoulos, J. Nieto-Camero, D.J. Parker, G. Poludniowski, T. Price, C. Waltham, N.M. Allinson, '''CMOS Active Pixel Sensors as energy-range detectors for proton Computed Tomography''', Journal of Instrumentation. 10 (2015) C06001–C06001. doi:10.1088/1748-0221/10/06/C06001.
* M. Esposito, T. Anaxagoras, A. Fant, K. Wells, A. Konstantinidis, J.P.F. Osmond, P.M. Evans, R.D. Speller, N.M. Allinson, '''DynAMITe: a wafer scale sensor for biomedical applications''', Journal of Instrumentation. 6 (2011) C12064–C12064. doi:10.1088/1748-0221/6/12/C12064.
* T. Price, M. Esposito, G. Poludniowski, J. Taylor, C. Waltham, D.J. Parker, S. Green, S. Manolopoulos, N.M. Allinson, T. Anaxagoras, P. Evans, J. Nieto-Camero, '''Expected proton signal sizes in the PRaVDA Range Telescope for proton Computed Tomography''', Journal of Instrumentation. 10 (2015) P05013–P05013. doi:10.1088/1748-0221/10/05/P05013.
* G. Poludniowski, N.M. Allinson, P.M. Evans, '''Proton computed tomography reconstruction using a backprojection-then-filtering approach''', Physics in Medicine and Biology. 59 (2014) 7905–7918. doi:10.1088/0031-9155/59/24/7905.
* G. Poludniowski, N.M. Allinson, T. Anaxagoras, M. Esposito, S. Green, S. Manolopoulos, J. Nieto-Camero, D.J. Parker, T. Price, P.M. Evans, '''Proton-counting radiography for proton therapy: a proof of principle using CMOS APS technology''', Physics in Medicine and Biology. 59 (2014) 2569–2581. doi:10.1088/0031-9155/59/11/2569.

=== From Lomda Linda ===
* T. Plautz, V. Bashkirov, V. Feng, F. Hurley, R.P. Johnson, C. Leary, S. Macafee, A. Plumb, V. Rykalin, H.F.-W. Sadrozinski, K. Schubert, R. Schulte, B. Schultze, D. Steinberg, M. Witt, A. Zatserklyaniy, '''200 MeV Proton Radiography Studies With a Hand Phantom Using a Prototype Proton CT Scanner''', IEEE Transactions on Medical Imaging. 33 (2014) 875–881. doi:10.1109/TMI.2013.2297278.
* R. P. Johnson, V. Bashkirov, L. DeWitt, V. Giacometti, R. F. Hurley, P. Piersimoni, T. E. Plautz, H. F. W. Sadrozinski, K. Schubert, R. Schulte, B. Schultze, A. Zatserklyaniy, '''A Fast Experimental Scanner for Proton CT: Technical Performance and First Experience With Phantom Scans''', IEEE Transactions on Nuclear Science. 63 (2016) 52–60. doi:10.1109/TNS.2015.2491918.
* R. Schulte, V. Bashkirov, T. Li, Z. Liang, K. Mueller, J. Heimann, L.R. Johnson, B. Keeney, H.-W. Sadrozinski, A. Seiden, others, '''Conceptual design of a proton computed tomography system for applications in proton radiation therapy''', Nuclear Science, IEEE Transactions on. 51 (2004) 866–872.
* H.-W. Sadrozinski, R.P. Johnson, S. Macafee, A. Plumb, D. Steinberg, A. Zatserklyaniy, V.A. Bashkirov, R.F. Hurley, R.W. Schulte, '''Development of a head scanner for proton CT''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 699 (2013) 205–210.
* H.-W. Sadrozinski, V. Bashkirov, M. Bruzzi, L.R. Johnson, B. Keeney, G. Ross, R.W. Schulte, A. Seiden, K. Shahnazi, D.C. Williams, others, '''Issues in proton computed tomography''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 511 (2003) 275–281.
* R.W. Schulte, A.J. Wroe, '''New developments in treatment planning and verification of particle beam therapy''', Translational Cancer Research. 1 (2012) 184–195.
* V.A. Bashkirov, R.W. Schulte, R.F. Hurley, R.P. Johnson, H.F.-W. Sadrozinski, A. Zatserklyaniy, T. Plautz, V. Giacometti, '''Novel scintillation detector design and performance for proton radiography and computed tomography''', Medical Physics. 43 (2016) 664–674. doi:10.1118/1.4939255.
* R.W. Schulte, V. Bashkirov, R. Johnson, H.-W. Sadrozinski, K.E. Schubert, '''Overview of the LLUMC/UCSC/CSUSB Phase 2 Proton CT Project''', Transactions of the American Nuclear Society. 106 (2012) 59.
* R. Johnson, V.A. Bashkirov, V. Giacometti, R.F. Hurley, P. Piersimoni, T. Plautz, '''Results from a pre-clinical head scanner for proton CT''', (2014).
* R.F. Hurley, R.W. Schulte, V.A. Bashkirov, G. Coutrakon, H.-W. Sadrozinski, B. Patyal, '''The Phase I Proton CT Scanner and Test Beam Results at LLUMC''', invited, Transactions of the American Nuclear Society. 106 (2012) 63.
* R.P. Johnson, J. DeWitt, C. Holcomb, S. Macafee, H.F.-W. Sadrozinski, D. Steinberg, '''Tracker Readout ASIC for Proton Computed Tomography Data Acquisition''', IEEE Transactions on Nuclear Science. 60 (2013) 3262–3269. doi:10.1109/TNS.2013.2274663.
* R.F. Hurley, R.W. Schulte, V.A. Bashkirov, A.J. Wroe, A. Ghebremedhin, H.F.-W. Sadrozinski, V. Rykalin, G. Coutrakon, P. Koss, B. Patyal, '''Water-equivalent path length calibration of a prototype proton CT scanner''', Medical Physics. 39 (2012) 2438. doi:10.1118/1.3700173.

=== From the NIU project (using scitillating fibres) ===
* M. Naimuddin, G. Coutrakon, G. Blazey, S. Boi, A. Dyshkant, B. Erdelyi, D. Hedin, E. Johnson, J. Krider, V. Rukalin, others, '''Development of a proton Computed Tomography detector system''', Journal of Instrumentation. 11 (2016) C02012.
* S.A. Uzunyan, G. Blazey, S. Boi, G. Coutrakon, A. Dyshkant, B. Erdelyi, A. Gearhart, D. Hedin, E. Johnson, J. Krider, others, '''Development of a proton Computed Tomography (pCT) scanner at NIU''', arXiv Preprint arXiv:1312.3977. (2013). http://arxiv.org/abs/1312.3977 (accessed January 15, 2015).

=== From the PRIMA project at INFN ===
* M. Scaringella, M. Bruzzi, M. Bucciolini, M. Carpinelli, G.A.P. Cirrone, C. Civinini, G. Cuttone, D.L. Presti, S. Pallotta, C. Pugliatti, N. Randazzo, F. Romano, V. Sipala, C. Stancampiano, C. Talamonti, E. Vanzi, M. Zani, '''A proton Computed Tomography based medical imaging system''', Journal of Instrumentation. 9 (2014) C12009–C12009. doi:10.1088/1748-0221/9/12/C12009.
* C. Civinini, M. Bruzzi, M. Bucciolini, M. Carpinelli, G.A.P. Cirrone, G. Cuttone, D. Lo Presti, S. Pallotta, C. Pugliatti, N. Randazzo, others, '''Recent results on the development of a proton computed tomography system''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 732 (2013) 573–576.
* E. Vanzi, M. Bruzzi, M. Bucciolini, G.A.P. Cirrone, C. Civinini, G. Cuttone, D. Lo Presti, S. Pallotta, C. Pugliatti, N. Randazzo, F. Romano, M. Scaringella, V. Sipala, C. Stancampiano, C. Talamonti, M. Zani, '''The PRIMA collaboration: Preliminary results in FBP reconstruction of pCT data''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 730 (2013) 184–190. doi:10.1016/j.nima.2013.05.193.
* M. Scaringella, M. Brianzi, M. Bruzzi, M. Bucciolini, M. Carpinelli, G.A.P. Cirrone, C. Civinini, G. Cuttone, D. Lo Presti, S. Pallotta, others, '''The PRIMA (Proton Imaging) collaboration: development of a proton Computed Tomography apparatus''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 730 (2013) 178–183.
* V. Sipala, N. Randazzo, D.L. Presti, C. Stancampiano, M. Bruzzi, M. Bucciolini, S. Pallotta, M. Scaringella, C. Talamonti, M. Tesi, others, '''Upgrade of the proton Computed Tomography system of the PRIMA project''', PoS (RD11). 13 (2011). http://www.researchgate.net/publication/230709286_Upgrade_of_the_proton_Computed_Tomography_system_of_the_PRIMA_project_Speaker/file/9fcfd5034f8b703175.pdf (accessed January 15, 2015).

=== From the proton radiography project at Heidelberg ===
* I. Rinaldi, S. Brons, O. Jäkel, B. Voss, K. Parodi, '''A method to increase the nominal range resolution of a stack of parallel-plate ionization chambers''', Physics in Medicine and Biology. 59 (2014) 5501–5515. doi:10.1088/0031-9155/59/18/5501.
* C. Kurz, A. Mairani, K. Parodi, '''First experimental-based characterization of oxygen ion beam depth dose distributions at the Heidelberg Ion-Beam Therapy Center''', Physics in Medicine and Biology. 57 (2012) 5017–5034. doi:10.1088/0031-9155/57/15/5017.

=== (Historical) proton radiography at PSI ===
* P. Pemler, J. Besserer, J. De Boer, M. Dellert, C. Gahn, M. Moosburger, U. Schneider, E. Pedroni, H. Stäuble, '''A detector system for proton radiography on the gantry of the Paul-Scherrer-Institute''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 432 (1999) 483–495.
* N.S.P. King, E. Ables, K. Adams, K.R. Alrick, J.F. Amann, S. Balzar, P.D. Barnes Jr, M.L. Crow, S.B. Cushing, J.C. Eddleman, others, '''An 800-MeV proton radiography facility for dynamic experiments''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 424 (1999) 84–91.
* S. Braccini, A. Ereditato, I. Kreslo, U. Moser, C. Pistillo, S. Studer, P. Scampoli, A. Coray, E. Pedroni, '''First results on proton radiography with nuclear emulsion detectors''', Journal of Instrumentation. 5 (2010) P09001.
* S. Braccini, A. Ereditato, I. Kreslo, U. Moser, C. Pistillo, P. Scampoli, S. Studer, '''Nuclear Emulsion Film Detectors for Proton Radiography: Design and Test of the First Prototype''', arXiv Preprint arXiv:1001.0857. (2010). http://arxiv.org/abs/1001.0857 (accessed January 15, 2015).

== Interesting theses on proton CT ==
* P.C. Tsopelas, '''Applying GridPix as 3D particle tracker for proton radiography''', MSc, University of Utrecht, 2011. https://wiki.nikhef.nl/detector/pub/Main/ArticlesAndTalks/Panagiotis_Tsopelas_Master_Thesis.pdf (accessed January 12, 2015).
* E. Hansen, '''Charge diffusion modelling for a monolithic active pixel sensor detector with application to proton CT''', BSc Project work, NTNU, 2016.
* M. Yang, '''Dual Energy computed tomography for proton therapy treatment planning''', PhD, University of Texas, 2011.
* S.N. Penfold, '''Image reconstruction and Monte Carlo simulations in the development of proton computed tomography for applications in proton radiation therpy''', PhD, University of Wollongong, 2010.
* D.C. Hansen, '''Improving Ion Computed Tomography''', PhD, Aarhus Universitet, 2014. http://pure.au.dk/portal/files/83515131/dissertation.pdf (accessed January 12, 2015).
* L. Maczewski, '''Measurements and simulations of MAPS (Monolithic Active Pixel Sensors) response to charged particles - a study towards a vertex detector at the ILC''', PhD, 2010. http://arxiv.org/abs/1005.3710 (accessed January 12, 2015).

== On the ALPIDE chip ==
* M. Mager, '''ALPIDE, the Monolithic Active Pixel Sensor for the ALICE ITS upgrade''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 824 (2016) 434–438. doi:10.1016/j.nima.2015.09.057.
* C. Cavicchioli, P.L. Chalmet, P. Giubilato, H. Hillemanns, A. Junique, T. Kugathasan, M. Mager, C.A. Marin Tobon, P. Martinengo, S. Mattiazzo, H. Mugnier, L. Musa, D. Pantano, J. Rousset, F. Reidt, P. Riedler, W. Snoeys, J.W. Van Hoorne, P. Yang, '''Design and characterization of novel monolithic pixel sensors for the ALICE ITS upgrade''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 765 (2014) 177–182. doi:10.1016/j.nima.2014.05.027.
* G. Aglieri Rinella, '''The ALPIDE pixel sensor chip for the upgrade of the ALICE Inner Tracking System''', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. (2016). doi:10.1016/j.nima.2016.05.016.

Main Page

2018-03-09T09:47:19Z

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Main Page

2018-03-09T09:46:24Z

Hpe090: Added theses to publications

File:A digital tracking calorimeter for proton computed tomography.pdf

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Workshops

2018-03-09T09:08:11Z

Hpe090: /* 07 - 08.03 in Bergen */

== 2016 ==
=== 22.11.-23.11. in Bergen ===

Agenda 

Tuesday, 22.11.: Presentations 

09.00 Bergen pCT – Dieter 

09.30 Padua pCT – Piero 

10.00 [[:File:workshop 2016-11 beam test results.pdf | Beam test results with FOCAL prototype - Helge]] 

11.15 [[:File:workshop 2016-11 MC simulations Helge.pdf | Simulations – Ilker (+ Helge + Jarle)]]
 

12:00 Software infrastructure – Boris 

13.30 [[Media:2016-11-22_Pettersen_PCT_reconstruction.pdf | Proton CT reconstruction, Helge E. S. Pettersen]] 

Hardware 

14.00 Radiation levels - Jarle 

14.45 Hardware: sensors, mechanical & electrical integration 

15.15 Readout concept - Haakon 

Wednesday, 23.11.: Hands-on 

09.00 pCT simulation & pCT reconstruction software 

Minutes: [[:File:pCT_planning_Nov_2016.pdf]]

* ASK slides direct here or link to new page
* [[Media:Imeric_simulation_pCT_workshop_22_11_2016.pdf | Monte Carlo code overview and comparison, Ilker Meric]]

== 2017 ==
=== 15.09. in Bergen ===

Agenda 

Friday, 15.09.: Presentations 

09.00 – 09.20 WP5 – Chip integration onto PCBs (D. Röhrich)

09.20 – 10.10 WP1 – [[:File:2017-09-15 workshop Helge Pettersen.pdf | Monte Carlo simulations for the optimization of detector geometry (H. E. S. Pettersen)]]

10.10 – 10.35 WP1 – [[:File:RadiationEnvironment_Electronics.pdf | Monte Carlo simulations of the expected radiation environment, Jarle Rambo Sølie (Slide 17 and 18 contains new '''flux''' calculations for the FPGAs)]]

10.30 – 10.40 Break

10.40 – 11.00 WP3 – [[:File:pCT Workshop Presentation - 15 sept 2017.pdf | Initial considerations for the pCT readout (O. Grøttvik) ]]

11.00 – 11.45 WP7 – [[:File:2017-09-15_pctbergen_mlp.pdf | Most likely path (MLP) estimation (M. Richter)]]

11.45 – 12.00 WP5 – Potential cooling schemes (H. Shafiee)

12.00 – 12.30 Lunch break

12.30 – 14.00 WP meetings (Each WP plans activities for the rest of the year)

14.00 – 16.00 Group discussion (meeting back in the bachelor room)

* [[:File:WP5, Potential cooling & Heat transfer.pdf | WP5 - Potential cooling schemes & heat transfer, Hesam Shafiee]]

=== 06.11 - 07.11 in Bergen / Meeting with UU ===

Monday, 06.11., room 456, IFT:

09:30 – 10:15 [[:File:Chania_2017_pCT.pdf | General Overview (Dieter)]]

10:15 – 11:15 [[:File:Detector layout specifications.pdf | Detector layout specification (Helge)]]

11:30 – 12:00 [[:File:RadiationEnvironment_06-11.pdf | Radiation environment (Jarle)]]

13:00 – 16:00 Mounting of chips on PCBs
* [[:File:IB_FPC_DiMauro-R260417.pdf | ITS wire bonding technique ]]
* [[:File:pCT meeting -LTU-NIKHEF 2017 11 06-7-F.pdf | Alternative technique - tab bonding, chipcable (Ton, Slava, Ihor)]]

Tuesday, 07.11., room 456, IFT:

09:00 – 12:00 Discussions on mechanical aspects of the pCT prototype
* [[:File:Potential cooling schemes, pCT workshop 2.pdf | Potential Cooling Schemes for the pCT prototype (Hesam)]]

13:00 – 14:00 [[:File:pCT Presentation - 7 nov 2017.pdf | Interface to readout electronic (Ola)]]

14:00 – 16:00 Towards a FoCal prototype

07.03 Wednesday (Teaching lab 260, Department of Physics and Technology, University of Bergen)

== 2018 ==
=== 07 - 08.03 in Bergen ===

'''07.03 Wednesday (Teaching lab 260, Department of Physics and Technology, University of Bergen)'''

09.30 – 09.45 Welcome (Dieter R.)

09.45 – 10.15 Sensor characterization; beam test results of sensor chips (Andreas S. , data from Australia / Susmita A., Viljar E., data from Oslo, WP2)

10.15 – 10.45 [[:File:workshop-helge-pettersen-2018-03-07.pdf | Latest on the detector simulations / Detector design specs. (Helge)]]

10.45 – 11.00 Coffee break

11.00 – 11.30 [[:File:07MarchMLP.pdf | Initial MLP implementations / considerations (Jarle)]]

11.30 – 12.00 Updates on computing environment / DAQ system (WP4)

12.00 – 13.00 Lunch

13.00 – 14.00 [[:File:Workshop-Hesam-Shafiee-2018-03-07.pdf | Updates on the mechanical design: support structure + cooling (Hesam)]]

14.00 – 15.00 Updates on the development of read-out electronics (WP3)

15.00 – 16.00 Outlook and discussions

'''08.03 Thursday (Bachelorrommet, 3rd floor, Department of Physics and Technology, University of Bergen)'''

09.30 – 10.30 Short presentations of the ongoing MSc projects with relevance to the pCT-project

10.30 – 11.30 Activities of Kharkiv team for pCT/FoCal projects: current status (Ihor T.)

11.30 – 12.00 Introduction to topological data analysis (Nello B.)

12.00 – 12.30 Discussions on applications of topological data analysis to pCT

12.30 – 16.00 Rest of the day is reserved for WP-meetings. Those WPs with interdependencies should have meetings with each other to clarify challenges and plan activities.

Workshops

2018-03-08T08:44:38Z

Hpe090: /* 07 - 08.03 in Bergen */

== 2016 ==
=== 22.11.-23.11. in Bergen ===

Agenda 

Tuesday, 22.11.: Presentations 

09.00 Bergen pCT – Dieter 

09.30 Padua pCT – Piero 

10.00 [[:File:workshop 2016-11 beam test results.pdf | Beam test results with FOCAL prototype - Helge]] 

11.15 [[:File:workshop 2016-11 MC simulations Helge.pdf | Simulations – Ilker (+ Helge + Jarle)]]
 

12:00 Software infrastructure – Boris 

13.30 [[Media:2016-11-22_Pettersen_PCT_reconstruction.pdf | Proton CT reconstruction, Helge E. S. Pettersen]] 

Hardware 

14.00 Radiation levels - Jarle 

14.45 Hardware: sensors, mechanical & electrical integration 

15.15 Readout concept - Haakon 

Wednesday, 23.11.: Hands-on 

09.00 pCT simulation & pCT reconstruction software 

Minutes: [[:File:pCT_planning_Nov_2016.pdf]]

* ASK slides direct here or link to new page
* [[Media:Imeric_simulation_pCT_workshop_22_11_2016.pdf | Monte Carlo code overview and comparison, Ilker Meric]]

== 2017 ==
=== 15.09. in Bergen ===

Agenda 

Friday, 15.09.: Presentations 

09.00 – 09.20 WP5 – Chip integration onto PCBs (D. Röhrich)

09.20 – 10.10 WP1 – [[:File:2017-09-15 workshop Helge Pettersen.pdf | Monte Carlo simulations for the optimization of detector geometry (H. E. S. Pettersen)]]

10.10 – 10.35 WP1 – [[:File:RadiationEnvironment_Electronics.pdf | Monte Carlo simulations of the expected radiation environment, Jarle Rambo Sølie (Slide 17 and 18 contains new '''flux''' calculations for the FPGAs)]]

10.30 – 10.40 Break

10.40 – 11.00 WP3 – [[:File:pCT Workshop Presentation - 15 sept 2017.pdf | Initial considerations for the pCT readout (O. Grøttvik) ]]

11.00 – 11.45 WP7 – [[:File:2017-09-15_pctbergen_mlp.pdf | Most likely path (MLP) estimation (M. Richter)]]

11.45 – 12.00 WP5 – Potential cooling schemes (H. Shafiee)

12.00 – 12.30 Lunch break

12.30 – 14.00 WP meetings (Each WP plans activities for the rest of the year)

14.00 – 16.00 Group discussion (meeting back in the bachelor room)

* [[:File:WP5, Potential cooling & Heat transfer.pdf | WP5 - Potential cooling schemes & heat transfer, Hesam Shafiee]]

=== 06.11 - 07.11 in Bergen / Meeting with UU ===

Monday, 06.11., room 456, IFT:

09:30 – 10:15 [[:File:Chania_2017_pCT.pdf | General Overview (Dieter)]]

10:15 – 11:15 [[:File:Detector layout specifications.pdf | Detector layout specification (Helge)]]

11:30 – 12:00 [[:File:RadiationEnvironment_06-11.pdf | Radiation environment (Jarle)]]

13:00 – 16:00 Mounting of chips on PCBs
* [[:File:IB_FPC_DiMauro-R260417.pdf | ITS wire bonding technique ]]
* [[:File:pCT meeting -LTU-NIKHEF 2017 11 06-7-F.pdf | Alternative technique - tab bonding, chipcable (Ton, Slava, Ihor)]]

Tuesday, 07.11., room 456, IFT:

09:00 – 12:00 Discussions on mechanical aspects of the pCT prototype
* [[:File:Potential cooling schemes, pCT workshop 2.pdf | Potential Cooling Schemes for the pCT prototype (Hesam)]]

13:00 – 14:00 [[:File:pCT Presentation - 7 nov 2017.pdf | Interface to readout electronic (Ola)]]

14:00 – 16:00 Towards a FoCal prototype

07.03 Wednesday (Teaching lab 260, Department of Physics and Technology, University of Bergen)

== 2018 ==
=== 07 - 08.03 in Bergen ===

'''07.03 Wednesday (Teaching lab 260, Department of Physics and Technology, University of Bergen)'''

09.30 – 09.45 Welcome (Dieter R.)

09.45 – 10.15 Sensor characterization; beam test results of sensor chips (Andreas S. , data from Australia / Susmita A., Viljar E., data from Oslo, WP2)

10.15 – 10.45 [[:File:workshop-helge-pettersen-2018-03-07.pdf | Latest on the detector simulations / Detector design specs. (Helge)]]

10.45 – 11.00 Coffee break

11.00 – 11.30 [[:File:07MarchMLP.pdf | Initial MLP implementations / considerations (Jarle)]]

11.30 – 12.00 Updates on computing environment / DAQ system (WP4)

12.00 – 13.00 Lunch

13.00 – 14.00 Updates on the mechanical design (support structure + cooling) (WP5)

14.00 – 15.00 Updates on the development of read-out electronics (WP3)

15.00 – 16.00 Outlook and discussions

'''08.03 Thursday (Bachelorrommet, 3rd floor, Department of Physics and Technology, University of Bergen)'''

09.30 – 10.30 Short presentations of the ongoing MSc projects with relevance to the pCT-project

10.30 – 11.30 Activities of Kharkiv team for pCT/FoCal projects: current status (Ihor T.)

11.30 – 12.00 Introduction to topological data analysis (Nello B.)

12.00 – 12.30 Discussions on applications of topological data analysis to pCT

12.30 – 16.00 Rest of the day is reserved for WP-meetings. Those WPs with interdependencies should have meetings with each other to clarify challenges and plan activities.

Workshops

2018-03-08T08:40:19Z

Hpe090: Added workshop 07-03 march 2018

== 2016 ==
=== 22.11.-23.11. in Bergen ===

Agenda 

Tuesday, 22.11.: Presentations 

09.00 Bergen pCT – Dieter 

09.30 Padua pCT – Piero 

10.00 [[:File:workshop 2016-11 beam test results.pdf | Beam test results with FOCAL prototype - Helge]] 

11.15 [[:File:workshop 2016-11 MC simulations Helge.pdf | Simulations – Ilker (+ Helge + Jarle)]]
 

12:00 Software infrastructure – Boris 

13.30 [[Media:2016-11-22_Pettersen_PCT_reconstruction.pdf | Proton CT reconstruction, Helge E. S. Pettersen]] 

Hardware 

14.00 Radiation levels - Jarle 

14.45 Hardware: sensors, mechanical & electrical integration 

15.15 Readout concept - Haakon 

Wednesday, 23.11.: Hands-on 

09.00 pCT simulation & pCT reconstruction software 

Minutes: [[:File:pCT_planning_Nov_2016.pdf]]

* ASK slides direct here or link to new page
* [[Media:Imeric_simulation_pCT_workshop_22_11_2016.pdf | Monte Carlo code overview and comparison, Ilker Meric]]

== 2017 ==
=== 15.09. in Bergen ===

Agenda 

Friday, 15.09.: Presentations 

09.00 – 09.20 WP5 – Chip integration onto PCBs (D. Röhrich)

09.20 – 10.10 WP1 – [[:File:2017-09-15 workshop Helge Pettersen.pdf | Monte Carlo simulations for the optimization of detector geometry (H. E. S. Pettersen)]]

10.10 – 10.35 WP1 – [[:File:RadiationEnvironment_Electronics.pdf | Monte Carlo simulations of the expected radiation environment, Jarle Rambo Sølie (Slide 17 and 18 contains new '''flux''' calculations for the FPGAs)]]

10.30 – 10.40 Break

10.40 – 11.00 WP3 – [[:File:pCT Workshop Presentation - 15 sept 2017.pdf | Initial considerations for the pCT readout (O. Grøttvik) ]]

11.00 – 11.45 WP7 – [[:File:2017-09-15_pctbergen_mlp.pdf | Most likely path (MLP) estimation (M. Richter)]]

11.45 – 12.00 WP5 – Potential cooling schemes (H. Shafiee)

12.00 – 12.30 Lunch break

12.30 – 14.00 WP meetings (Each WP plans activities for the rest of the year)

14.00 – 16.00 Group discussion (meeting back in the bachelor room)

* [[:File:WP5, Potential cooling & Heat transfer.pdf | WP5 - Potential cooling schemes & heat transfer, Hesam Shafiee]]

=== 06.11 - 07.11 in Bergen / Meeting with UU ===

Monday, 06.11., room 456, IFT:

09:30 – 10:15 [[:File:Chania_2017_pCT.pdf | General Overview (Dieter)]]

10:15 – 11:15 [[:File:Detector layout specifications.pdf | Detector layout specification (Helge)]]

11:30 – 12:00 [[:File:RadiationEnvironment_06-11.pdf | Radiation environment (Jarle)]]

13:00 – 16:00 Mounting of chips on PCBs
* [[:File:IB_FPC_DiMauro-R260417.pdf | ITS wire bonding technique ]]
* [[:File:pCT meeting -LTU-NIKHEF 2017 11 06-7-F.pdf | Alternative technique - tab bonding, chipcable (Ton, Slava, Ihor)]]

Tuesday, 07.11., room 456, IFT:

09:00 – 12:00 Discussions on mechanical aspects of the pCT prototype
* [[:File:Potential cooling schemes, pCT workshop 2.pdf | Potential Cooling Schemes for the pCT prototype (Hesam)]]

13:00 – 14:00 [[:File:pCT Presentation - 7 nov 2017.pdf | Interface to readout electronic (Ola)]]

14:00 – 16:00 Towards a FoCal prototype

07.03 Wednesday (Teaching lab 260, Department of Physics and Technology, University of Bergen)

== 2018 ==
=== 07 - 08.03 in Bergen ===

09.30 – 09.45 Welcome (Dieter R.)

09.45 – 10.15 Sensor characterization; beam test results of sensor chips (Andreas S. , data from Australia / Susmita A., Viljar E., data from Oslo, WP2)

10.15 – 10.45 [[:File:workshop-helge-pettersen-2018-03-07.pdf | Latest on the detector simulations / Detector design specs. (Helge)]]

10.45 – 11.00 Coffee break

11.00 – 11.30 Initial MLP implementations / considerations (WP1)

11.30 – 12.00 Updates on computing environment / DAQ system (WP4)

12.00 – 13.00 Lunch

13.00 – 14.00 Updates on the mechanical design (support structure + cooling) (WP5)

14.00 – 15.00 Updates on the development of read-out electronics (WP3)

15.00 – 16.00 Outlook and discussions

08.03 Thursday (Bachelorrommet, 3rd floor, Department of Physics and Technology, University of Bergen)

09.30 – 10.30 Short presentations of the ongoing MSc projects with relevance to the pCT-project

10.30 – 11.30 Activities of Kharkiv team for pCT/FoCal projects: current status (Ihor T.)

11.30 – 12.00 Introduction to topological data analysis (Nello B.)

12.00 – 12.30 Discussions on applications of topological data analysis to pCT

12.30 – 16.00 Rest of the day is reserved for WP-meetings. Those WPs with interdependencies should have meetings with each other to clarify challenges and plan activities.

File:Workshop-helge-pettersen-2018-03-07.pdf

2018-03-08T08:39:40Z

Hpe090: File uploaded with MsUpload

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Main Page

2017-12-21T10:02:19Z

Hpe090: /* Published */

WP1 Ideas for project to pursue

2017-11-23T07:07:29Z

Hpe090: /* Re-implementation of Maczewski model to analytically describe charge diffusion process */

Below is a list of ideas regarding DTC data analysis, design etc. that might be worthwhile to pursue.

== Time-dependence of charge diffusion process ==
We see in the ALPIDE chips that the quick integration time of ~10 µs reveals a time dependence on the charge diffusion process -- i.e. that too small clusters, medium clusters and then large clusters with holes are visible. It would be interesting to see if it's possible to use the data already acquired to model the time dependency in this process.

== Re-implementation of Maczewski model to analytically describe charge diffusion process ==
The model as it stands today looks like below, which does not accurately describe the data.

[[File:cs-vs-edep.JPG|400px]]

Two shortcomings of the Maczewski model (see [http://arxiv.org/abs/1005.3710 his thesis] and [https://brage.bibsys.no/xmlui/handle/11250/2434108 Even's MSc thesis]) are that
# Only one term in the expansion is used (the model was used as in Maczewski's thesis). I'm not sure how this is a shortcoming, but Even who modeled this claimed that it could be improved.
# The Most Probable Value of the Landau distribution of Energy Deposition values in the epitaxial value was considered. This is a more serious approximation, and a new implementation should be made based on Even's code that rather samples from a Landau distribution.

== PID for DTC ==
Intuitively, it should be possible to perform a PID (Particle ID) together with the track reconstruction in the DTC. Different particles (w/different charge) should have a different edep distribution in the epitaxial layer, giving rise to depth-dependent cluster size distributions (depth dose) of different values. The height of the plataeu region of the Bragg Curve is then the PID indicator: H, He, C, ...
This would e.g. be of help during alpha beam tests, where secondary protons from the phantom easily could be removed.
* Helge wants to further explore this idea and if good make a conference paper on this + the charge diffusion model modeled on the data we already have -- and/or on ALPIDE.
* Bias voltage dependency..?

== Local-to-Global Monte Carlo simulations for quick MLP ==
Local-to-Global MC is a method that was introduced in the early 90's for electron transport simulations for electron radiotherapy treatment planning systems. The idea was to gain speed in MC calculations of the dose distribution. The method is based on simulations of electron transport in local geometries, so-called "kugels", i.e. "spheres", of varying material compositions, dimensions and obviously, electron energies. In its simplest form, ignoring secondary particle production, electrons are initiated at the center of a given "kugel". The electron exit angles, positions and energies, i.e. the exiting electron's "phase space", are then tallied. The procedure is repeated for different materials, "kugel" sizes and electron energies. The resulting distributions are stored in memory generating the so-called probability distribution functions. Then, in the global geometry, the electron simulations are accelerated through the use of these "kugels" and the corresponding probability distributions from which random samples are drawn. The method has previously been successfully applied to electron radiotherapy. More on the results and the method itself can be found here https://digital.library.unt.edu/ark:/67531/metadc682086/m2/1/high_res_d/39026.pdf. The Local-to-Global MC methods have, however, been abandoned due to the affordability of powerful CPUs and GPUs.

An important point is, however, that the method could, in principle, be applied to the Most-Likely Path (MLP) estimation in proton CT. "Kugels" of varying materials and sizes can be simulated with varying proton energies to generate probability distributions. These local geometries can then be used to track protons through the patient geometry. An obvious advantage of the method over the more conventional methods would be the possibility of taking into account heterogeneous patient geometries. It will be a tedious step to generate the required probability distributions. However, it would be of utmost interest to implement this idea and compare it to conventional techniques used for the MLP estimations such as those based on log-likelihood maximization.

WP1 Ideas for project to pursue

2017-11-23T07:07:19Z

Hpe090: /* Re-implementation of Maczewski model to analytically describe charge diffusion process */

Below is a list of ideas regarding DTC data analysis, design etc. that might be worthwhile to pursue.

== Time-dependence of charge diffusion process ==
We see in the ALPIDE chips that the quick integration time of ~10 µs reveals a time dependence on the charge diffusion process -- i.e. that too small clusters, medium clusters and then large clusters with holes are visible. It would be interesting to see if it's possible to use the data already acquired to model the time dependency in this process.

== Re-implementation of Maczewski model to analytically describe charge diffusion process ==
The model as it stands today looks like below, which does not accurately describe the data.

[[File:cs-vs-edep.JPG|400px]]

Two shortcomings of the Maczewski model (see [http://arxiv.org/abs/1005.3710 his thesis] and [https://brage.bibsys.no/xmlui/handle/11250/2434108 Even's MSc thesis]) are that
# Only one term in the expansion is used (the model was used as in Maczewski's thesis). I'm not sure how this is a shortcoming, but Even how modeled this claimed that it could be improved.
# The Most Probable Value of the Landau distribution of Energy Deposition values in the epitaxial value was considered. This is a more serious approximation, and a new implementation should be made based on Even's code that rather samples from a Landau distribution.

== PID for DTC ==
Intuitively, it should be possible to perform a PID (Particle ID) together with the track reconstruction in the DTC. Different particles (w/different charge) should have a different edep distribution in the epitaxial layer, giving rise to depth-dependent cluster size distributions (depth dose) of different values. The height of the plataeu region of the Bragg Curve is then the PID indicator: H, He, C, ...
This would e.g. be of help during alpha beam tests, where secondary protons from the phantom easily could be removed.
* Helge wants to further explore this idea and if good make a conference paper on this + the charge diffusion model modeled on the data we already have -- and/or on ALPIDE.
* Bias voltage dependency..?

== Local-to-Global Monte Carlo simulations for quick MLP ==
Local-to-Global MC is a method that was introduced in the early 90's for electron transport simulations for electron radiotherapy treatment planning systems. The idea was to gain speed in MC calculations of the dose distribution. The method is based on simulations of electron transport in local geometries, so-called "kugels", i.e. "spheres", of varying material compositions, dimensions and obviously, electron energies. In its simplest form, ignoring secondary particle production, electrons are initiated at the center of a given "kugel". The electron exit angles, positions and energies, i.e. the exiting electron's "phase space", are then tallied. The procedure is repeated for different materials, "kugel" sizes and electron energies. The resulting distributions are stored in memory generating the so-called probability distribution functions. Then, in the global geometry, the electron simulations are accelerated through the use of these "kugels" and the corresponding probability distributions from which random samples are drawn. The method has previously been successfully applied to electron radiotherapy. More on the results and the method itself can be found here https://digital.library.unt.edu/ark:/67531/metadc682086/m2/1/high_res_d/39026.pdf. The Local-to-Global MC methods have, however, been abandoned due to the affordability of powerful CPUs and GPUs.

An important point is, however, that the method could, in principle, be applied to the Most-Likely Path (MLP) estimation in proton CT. "Kugels" of varying materials and sizes can be simulated with varying proton energies to generate probability distributions. These local geometries can then be used to track protons through the patient geometry. An obvious advantage of the method over the more conventional methods would be the possibility of taking into account heterogeneous patient geometries. It will be a tedious step to generate the required probability distributions. However, it would be of utmost interest to implement this idea and compare it to conventional techniques used for the MLP estimations such as those based on log-likelihood maximization.

WP1 Ideas for project to pursue

2017-11-16T08:18:03Z

Hpe090: /* PID for DTC */

WP1 Ideas for project to pursue

2017-11-16T08:17:05Z

Hpe090: /* Re-implementation of Maczewski model to analytically describe charge diffusion process */

WP1 Ideas for project to pursue

2017-11-16T08:16:58Z

Hpe090: Created page with "Below is a list of ideas regarding DTC data analysis, design etc. that might be worthwhile to pursue. == Time-dependence of charge diffusion process == We see in the ALPIDE c..."

File:Cs-vs-edep.JPG

2017-11-16T08:09:30Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

Workpackages

2017-11-16T08:02:49Z

Hpe090: /* WP1: Physics simulation, verification and design optimization */

ASK link to people responsible for package / sub package?

== [[WP1]]: Physics simulation, verification and design optimization ==
* Beam scenarios – beam spot, intensity
* Detector specifications: [[DTC optimization|Optimization of geometry and segmentation]]
* Radiation environment - location
* Evaluation of rates (average/worst case) of the digital backend of the sensor
* Beam tests of sensors
* [[WP1 Ideas for project to pursue]]

== [[WP2]]: Chip submission and sensor characterization ==
* Improved sensor and data encoding design
* Chip submission
* Testing of prototypes

== [[WP3]]: Data readout ==
* Optimisation of the readout electronics architecture
* SystemC simulation of rates (average/worst case) of the readout chain
* Development and testing of readout electronics
* Setting up a full readout chain
* Development of firmware and software

== [[WP4]]: Online systems ==
* Hardware infrastructure
* Software infrastructure
* DAQ software
* DCS + Trigger
* Data quality monitoring

== [[WP5]]: Assembly and System integration ==
* Assembly of chips into HICs/staves
* Assembly of staves into layers
* Integration of layers into a compact detector
* Mechanical and electrical integration, cooling
* Electronics and DAQ integration

== [[WP6]]: Commissioning ==
* Commissioning of the PRM in beams
* Performance evaluation in a pre-clinical environment, i.e. with phantoms

== [[WP7]]: Reconstruction software ==
* Calorimeter response
* Calorimeter track reconstruction
* Reconstruction of 3D trajectory – track vector matching
* 3D stopping power map

Workpackages

2017-11-16T08:02:41Z

Hpe090: /* WP1: Physics simulation, verification and design optimization */

ASK link to people responsible for package / sub package?

== [[WP1]]: Physics simulation, verification and design optimization ==
* Beam scenarios – beam spot, intensity
* Detector specifications: [[DTC optimization|Optimization of geometry and segmentation]]
* Radiation environment - location
* Evaluation of rates (average/worst case) of the digital backend of the sensor
* Beam tests of sensors
* [[Ideas for project to pursue]]

== [[WP2]]: Chip submission and sensor characterization ==
* Improved sensor and data encoding design
* Chip submission
* Testing of prototypes

== [[WP3]]: Data readout ==
* Optimisation of the readout electronics architecture
* SystemC simulation of rates (average/worst case) of the readout chain
* Development and testing of readout electronics
* Setting up a full readout chain
* Development of firmware and software

== [[WP4]]: Online systems ==
* Hardware infrastructure
* Software infrastructure
* DAQ software
* DCS + Trigger
* Data quality monitoring

== [[WP5]]: Assembly and System integration ==
* Assembly of chips into HICs/staves
* Assembly of staves into layers
* Integration of layers into a compact detector
* Mechanical and electrical integration, cooling
* Electronics and DAQ integration

== [[WP6]]: Commissioning ==
* Commissioning of the PRM in beams
* Performance evaluation in a pre-clinical environment, i.e. with phantoms

== [[WP7]]: Reconstruction software ==
* Calorimeter response
* Calorimeter track reconstruction
* Reconstruction of 3D trajectory – track vector matching
* 3D stopping power map

Main Page

2017-11-13T13:51:54Z

Hpe090: /* Workpackage Reports */

Main Page

2017-11-13T13:51:44Z

Hpe090: /* From WP1: */

File:PCT-WP1-1-Rev2 design recommendations.pdf

2017-11-13T13:51:16Z

Hpe090: File uploaded with MsUpload

File uploaded with MsUpload

Workshops

2017-11-09T09:33:58Z

Hpe090: /* 15.09. in Bergen */