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(Medical Imaging support)
m (Jaruga moved page Medical Imaging to Medical/Tasks/Imaging)
 
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Even if many open source components are currently available, Fedora is still lacking  
Even if many open source components are currently available, Fedora is still lacking proper medical imaging support.  
proper medical imaging support. This page is an attempt to coordinate the effort to provide the required packages.
This page is an attempt to coordinate the effort to provide the required packages.


In order to cover the gap we need to add:
What we already have in repositories:


* A free out-of-the-box working PACS solution.
* Orthanc, a free, lightweight PACS.
Picture Archiving and Communication Systems (PACS) provide the medical imaging world with economical storage, rapid retrieval of images, access to images acquired with multiple modalities, and simultaneous access at multiple sites. Electronic images and reports are transmitted digitally via PACS; this eliminates  the need to manually file, retrieve, or transport film jackets.
* dcmtk and gdcm which should cover almost all dicom necessity.
* octave-dicom a package to bring dicom support to octave.
* InsightToolkit which is a core dependency of many medical imaging software.
* OpenIGTLink which is used to connect to a medical tracker during surgery


* DICOM (Digital Imaging and Communications in Medicine) support
We are currently working on:
This is the universal format for PACS image storage and transfer.


* Viewers
* DICOM viewers like GinkoCAD.
Like [[http://www.osirix-viewer.com/ OsiriX]] for the Mac world
* (Semi-)Automatic segmentation programs such as ITKSnap.
* Image registration code such as Elastix.


* Imaging libraries specifically tailored for medical imaging
This table summarize the current status:




{|
{|
|- style=" color: #fff; background-color: #3074c2;"
|- style=" color: #fff; background-color: #3074c2;"
| '''Role''' || '''Proposed software''' || '''Link''' || '''Review''' || '''Comments'''
| '''Role''' || '''Proposed software''' || '''Trac Link'''  
|-
|-
| PACS || dcm4chee || http://www.dcm4che.org/ || - || Suggested by [[http://www.osirix-viewer.com/PACS.html OsiriX]]
| PACS || dcm4chee || https://fedorahosted.org/fedora-medical/ticket/11
|-
|  || orthanc || [[https://admin.fedoraproject.org/pkgdb/acls/name/orthanc Packaged]]
|-
| DICOM viewer || GinkGo-CADx || [[https://fedorahosted.org/fedora-medical/ticket/12 Free]]
|-
| DICOM toolkit || gdcm || [[https://admin.fedoraproject.org/pkgdb/acls/name/gdcm Packaged]]
|-
|  || octave-dicom || [[https://bugzilla.redhat.com/show_bug.cgi?id=962490 Packaged]]
|-  
|-  
|  || dcmtk || http://dicom.offis.de/dcmtk.php.en || [[https://bugzilla.redhat.com/show_bug.cgi?id=573910 573910]] ||
|  || dcmtk || [[https://admin.fedoraproject.org/pkgdb/acls/name/dcmtk Packaged]]
|-
| Image analysis library || InsightToolkit || [[https://fedorahosted.org/fedora-medical/ticket/10 Packaged]]
|-
|  || vmtk || https://fedorahosted.org/fedora-medical/ticket/18
|-
|  || openigtlink || [[https://admin.fedoraproject.org/pkgdb/acls/name/libigtl Packaged]]
|-
|  || ITK Tools || [[https://github.com/ITKTools/ITKTools Upstream]]
|-
|  || 3D Slicer || [[http://www.slicer.org/ Upstream]]
|-
|  || Image Guided Surgery Toolkit (IGSTK)  || [[http://www.igstk.org/ Upstream]]
|-
|-
|  || conquest || http://www.xs4all.nl/~ingenium/dicom.html || - ||
|  || Multi scale Toolkit (MSVTK)  || [[http://www.msvtk.org/ Upstream]]
|-
|-
| || cdmedic || http://cdmedicpacsweb.sourceforge.net/Home.html || - ||
| Rigid and non-rigid registration || elastix || [[https://fedorahosted.org/fedora-medical/ticket/8 Free]]
|-
|-
| DICOM viewer || kdradview || http://www.orcero.org/irbis/kradview/ || - || Seems dead
| || ANTS || https://fedorahosted.org/fedora-medical/ticket/19
|-
|-
| || aeskulap || http://aeskulap.nongnu.org/ || - || Seems dead
| Segmentation || ITKSnap || [[http://www.itksnap.org/pmwiki/pmwiki.php Upstream]]
|-
|-
| DICOM toolkit || gdcm || http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Main_Page || [[https://bugzilla.redhat.com/show_bug.cgi?id=566725 566725]] || Packaged
| || Seg3d 2 || [[http://www.sci.utah.edu/software/seg3d.html Upstream]] [[https://lists.fedorahosted.org/pipermail/medical-sig/2013-May/000281.html Blocked]]
|-
| Modelling || salome || https://fedorahosted.org/fedora-medical/ticket/20
|-
| FE/FV Solver || O-PALM || https://fedorahosted.org/fedora-medical/ticket/21
|-
|  || Elmer || https://fedorahosted.org/fedora-medical/ticket/22
|-
|  || Kratos || [[http://www.cimne.com/kratos/ Upstream]]
|-
|  || OpenFOAM || [[http://www.openfoam.com/ Upstream]]
|-
| Mesh || BioMesh3d || [[http://www.sci.utah.edu/software/biomesh3d.html Upstream]]
|-
|  || Cleaver || [[http://www.sci.utah.edu/software/cleaver.html Upstream]]
|-
| || Stellar || [[http://www.cs.berkeley.edu/~jrs/stellar/ Upstream]]
|-
| Shape model || ShapeWorks || [[http://www.sci.utah.edu/software/shapeworks.html Upstream]]
|-
|  || Statismo || [[https://github.com/statismo/statismo Upstream]]
|-
|-
| Image analysis library || itk || http://itk.org || [[https://bugzilla.redhat.com/show_bug.cgi?id=539387 539387]] ||


|}
|}

Latest revision as of 15:22, 1 March 2020

Even if many open source components are currently available, Fedora is still lacking proper medical imaging support. This page is an attempt to coordinate the effort to provide the required packages.

What we already have in repositories:

  • Orthanc, a free, lightweight PACS.
  • dcmtk and gdcm which should cover almost all dicom necessity.
  • octave-dicom a package to bring dicom support to octave.
  • InsightToolkit which is a core dependency of many medical imaging software.
  • OpenIGTLink which is used to connect to a medical tracker during surgery

We are currently working on:

  • DICOM viewers like GinkoCAD.
  • (Semi-)Automatic segmentation programs such as ITKSnap.
  • Image registration code such as Elastix.

This table summarize the current status:


Role Proposed software Trac Link
PACS dcm4chee https://fedorahosted.org/fedora-medical/ticket/11
orthanc [Packaged]
DICOM viewer GinkGo-CADx [Free]
DICOM toolkit gdcm [Packaged]
octave-dicom [Packaged]
dcmtk [Packaged]
Image analysis library InsightToolkit [Packaged]
vmtk https://fedorahosted.org/fedora-medical/ticket/18
openigtlink [Packaged]
ITK Tools [Upstream]
3D Slicer [Upstream]
Image Guided Surgery Toolkit (IGSTK) [Upstream]
Multi scale Toolkit (MSVTK) [Upstream]
Rigid and non-rigid registration elastix [Free]
ANTS https://fedorahosted.org/fedora-medical/ticket/19
Segmentation ITKSnap [Upstream]
Seg3d 2 [Upstream] [Blocked]
Modelling salome https://fedorahosted.org/fedora-medical/ticket/20
FE/FV Solver O-PALM https://fedorahosted.org/fedora-medical/ticket/21
Elmer https://fedorahosted.org/fedora-medical/ticket/22
Kratos [Upstream]
OpenFOAM [Upstream]
Mesh BioMesh3d [Upstream]
Cleaver [Upstream]
Stellar [Upstream]
Shape model ShapeWorks [Upstream]
Statismo [Upstream]
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