Table of Contents
(23 intermediate revisions by 4 users not shown) | |||
Line 1: | Line 1: | ||
+ | __TOC__ | ||
+ | |||
The following tables displays which modules are included in [[Special:FarsightDownloads|the latest stable release of Farsight]]. | The following tables displays which modules are included in [[Special:FarsightDownloads|the latest stable release of Farsight]]. | ||
− | = | + | = Table of Farsight Modules = |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
{| border="1" | {| border="1" | ||
|- bgcolor="#abcdef" | |- bgcolor="#abcdef" | ||
− | ! Module Name (click on the entries for a detailed description) !! What it does !! Contributors !! SVN?<sup>[1]</sup>!!CPack?<sup>[2]</sup>!!CTest?<sup>[3]</sup>!!Download | + | ! Module Name (click on the entries for a detailed description) !! What it does !! Contributors !! SVN?<sup>[1]</sup>!!CPack?<sup>[2]</sup>!!CTest?<sup>[3]</sup>!!Download!!Licensing Notes |
|- | |- | ||
| [[Registration_page#register_pair|register_pair]] | | [[Registration_page#register_pair|register_pair]] | ||
Line 38: | Line 16: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_pair.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_pair.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_pair.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_pair.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
| [[Registration_page#register_joint|register_joint]] | | [[Registration_page#register_joint|register_joint]] | ||
Line 46: | Line 25: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_joint.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_joint.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_joint.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_joint.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
| [[Registration_page#mosaic_images|mosaic_images]] | | [[Registration_page#mosaic_images|mosaic_images]] | ||
Line 54: | Line 34: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=mosaic_images.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=mosaic_images.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=mosaic_images.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=mosaic_images.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
| [[Registration_page#mosaic_image_pair|mosaic_image_pair]] | | [[Registration_page#mosaic_image_pair|mosaic_image_pair]] | ||
Line 62: | Line 43: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=mosaic_image_pair.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=mosaic_image_pair.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=mosaic_image_pair.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=mosaic_image_pair.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
| [[Registration_page#MontageNavigator|MontageNavigator]] | | [[Registration_page#MontageNavigator|MontageNavigator]] | ||
Line 70: | Line 52: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=MontageNavigator.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=MontageNavigator.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=MontageNavigator.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=MontageNavigator.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
|[[Nuclear Segmentation|segment_nuclei]] | |[[Nuclear Segmentation|segment_nuclei]] | ||
Line 78: | Line 61: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=segment_nuclei.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=segment_nuclei.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=segment_nuclei.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=segment_nuclei.exe&submit=Download win64] | ||
+ | |[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2]. | ||
|- | |- | ||
|[[Pattern Analysis Module]] | |[[Pattern Analysis Module]] | ||
Line 86: | Line 70: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=svm.zip&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=svm.zip&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=svm.zip&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=svm.zip&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
|[[FARSIGHT_Tutorials/5-Label#3D_Rendering|render]] | |[[FARSIGHT_Tutorials/5-Label#3D_Rendering|render]] | ||
Line 94: | Line 79: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=render.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=render.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=render.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=render.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
|[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]] | |[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]] | ||
Line 102: | Line 88: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=RPITrace3D.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=RPITrace3D.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=RPITrace3D.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=RPITrace3D.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
|[[SuperEllipseTrace3D]] | |[[SuperEllipseTrace3D]] | ||
Line 110: | Line 97: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=Trace3D.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=Trace3D.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=Trace3D.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=Trace3D.exe&submit=Download win64] | ||
− | + | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | |
|- | |- | ||
|[[Object_level_association]] | |[[Object_level_association]] | ||
Line 119: | Line 106: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=compute_associative_measures.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_associative_measures.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=compute_associative_measures.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_associative_measures.exe&submit=Download win64] | ||
+ | |[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2]. | ||
|- | |- | ||
|[[Features]] | |[[Features]] | ||
Line 127: | Line 115: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=compute_nuclei_features.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_nuclei_features.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=compute_nuclei_features.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_nuclei_features.exe&submit=Download win64] | ||
+ | |[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2]. | ||
|- | |- | ||
|[[TissueNets Program]] | |[[TissueNets Program]] | ||
Line 135: | Line 124: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=tissuenets.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_nuclei_features.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=tissuenets.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_nuclei_features.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
|[[Trace_Editor|trace_editor]] | |[[Trace_Editor|trace_editor]] | ||
Line 143: | Line 133: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=trace_editor.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=trace_editor.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=trace_editor.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=trace_editor.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
|- | |- | ||
|[[Vessel Laminae Segmentation]] | |[[Vessel Laminae Segmentation]] | ||
Line 151: | Line 142: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=vessel_segmentation.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=vessel_segmentation.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=vessel_segmentation.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=vessel_segmentation.exe&submit=Download win64] | ||
− | |[[ | + | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] |
− | |Segment | + | |- |
− | |[[User: | + | |[[NucleusEditor]] |
+ | |Segment, display, edit, and validate cell nuclei, generate different views of nuclei data | ||
+ | |[[User:Vargun|Isaac Abbot,Yousef Al-Kofahi,Aytekin Vargun]] | ||
|Y | |Y | ||
|Y | |Y | ||
|N | |N | ||
− | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile= | + | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=NucleusEditor.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=NucleusEditor.exe&submit=Download win64] |
+ | |[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2]. | ||
|- | |- | ||
|[[Fuzzy_Clustering]] | |[[Fuzzy_Clustering]] | ||
Line 166: | Line 160: | ||
|N | |N | ||
| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=run_fuzzy_clustering.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=run_fuzzy_clustering.exe&submit=Download win64] | | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=run_fuzzy_clustering.exe&submit=Download win32] [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=run_fuzzy_clustering.exe&submit=Download win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
+ | |- | ||
+ | | [[Program_Instruction#Code Components|Skel_streamline]] | ||
+ | | 3D Grayscale Image Skeletonization | ||
+ | | [[User:Xiaosong|Xiaosong Yuan]] | ||
+ | |Y | ||
+ | |N | ||
+ | |N | ||
+ | | [win32] [win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
+ | |- | ||
+ | | [[Program_Instruction#Code Components|MDL-constrained Grayscale Skeletonization]] | ||
+ | | Produce Complexity-constrained Dendritic Backbone and Spine Models | ||
+ | | [[User:Xiaosong|Xiaosong Yuan]] | ||
+ | |Y | ||
+ | |N | ||
+ | |N | ||
+ | | [win32] [win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
+ | |- | ||
+ | | [[ITK_Pre-Processing_Algorithm_Wrappers_in_Python|wrapper_itk_pre-processing]] | ||
+ | | Running python-based wrappers for ITK pre-processing algorithms (with GUI) | ||
+ | | [[User:Ramasa|Adarsh K. Ramasubramonian]] | ||
+ | |Y | ||
+ | |N | ||
+ | |N | ||
+ | |[win32] [win64] | ||
+ | |[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0] | ||
+ | |- | ||
+ | | [[Bio-Formats|Bio-Formats]] | ||
+ | | Standalone Java library for reading and writing life sciences image file formats. | ||
+ | | Curtis Rueden, Kevin Eliceiri | ||
+ | |Y | ||
+ | |N | ||
+ | |N | ||
+ | |[win32] [win64] | ||
+ | |[http://www.loci.wisc.edu/ome/formats-license.html GPL License] | ||
|} | |} | ||
Line 174: | Line 205: | ||
<sup>[3]</sup> Does this module utilize CTest to verify that its functionality works as intended? | <sup>[3]</sup> Does this module utilize CTest to verify that its functionality works as intended? | ||
+ | |||
+ | = How to maintain this Table = | ||
+ | |||
+ | Instructions for the team: I am trying to make sure that all of the modules that we have developed are: | ||
+ | |||
+ | * in the SVN repository | ||
+ | * in the CPack installable build | ||
+ | * described adequately in a wiki page that is linked (also a tutorial when possible). | ||
+ | |||
+ | We will do this one person at a time, and I will be in contact with each member of the team to get this | ||
+ | assembled. | ||
+ | |||
+ | Keep all table entries brief, not to exceed the size of a Tweet (i.e, 140 letters or less). The wiki page will | ||
+ | describe the module much more completely. | ||
+ | |||
+ | Don't worry about the order in which modules are listed for now. Eventually, they need to be in some | ||
+ | systematic order. | ||
+ | |||
+ | We'll be adding more columns to the table later. Your suggestions are welcome. My main concern | ||
+ | is to make sure that a biological user can make sense of the modules and know where to look | ||
+ | for more information on how to use them. Another concern is to make sure that external collaborators | ||
+ | are well positioned to contribute software modules to farsight in a way that is effective. | ||
+ | |||
+ | Badri. |
Latest revision as of 21:23, 16 November 2009
Contents |
The following tables displays which modules are included in the latest stable release of Farsight.
Table of Farsight Modules
[1] Is this module's source code checked into the Farsight subversion repository?
[2] Is this module included in the Farsight installer?
[3] Does this module utilize CTest to verify that its functionality works as intended?
How to maintain this Table
Instructions for the team: I am trying to make sure that all of the modules that we have developed are:
- in the SVN repository
- in the CPack installable build
- described adequately in a wiki page that is linked (also a tutorial when possible).
We will do this one person at a time, and I will be in contact with each member of the team to get this assembled.
Keep all table entries brief, not to exceed the size of a Tweet (i.e, 140 letters or less). The wiki page will describe the module much more completely.
Don't worry about the order in which modules are listed for now. Eventually, they need to be in some systematic order.
We'll be adding more columns to the table later. Your suggestions are welcome. My main concern is to make sure that a biological user can make sense of the modules and know where to look for more information on how to use them. Another concern is to make sure that external collaborators are well positioned to contribute software modules to farsight in a way that is effective.
Badri.