ShuttleTracker: Difference between revisions
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* Windows 64-bit installer: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-x86_win64-setup.exe shuttletracker-1.3.0-x86_win64-setup.exe]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY: This software was built with MSVC14 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2017 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY: The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.3.0-x86_win64-setup.exe is '''18d220e5d499239a50b75da2df68a05d'''.<br/></accordion> | * Windows 64-bit installer: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-x86_win64-setup.exe shuttletracker-1.3.0-x86_win64-setup.exe]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY: This software was built with MSVC14 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2017 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY: The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted shuttletracker-1.3.0-x86_win64-setup.exe is '''18d220e5d499239a50b75da2df68a05d'''.<br/></accordion> | ||
* macOS application bundle (zipped "app"): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-x86_64-darwin17.zip shuttletracker-1.3.0-x86_64-darwin17.zip]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY: This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY: MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.3.0-x86_64-darwin17.zip is ''' | * macOS application bundle (zipped "app"): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-x86_64-darwin17.zip shuttletracker-1.3.0-x86_64-darwin17.zip]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY: This software was built with XCode 8 and tested under macOS 10.13 (High Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY: MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted shuttletracker-1.3.0-x86_64-darwin17.zip is '''7cffa9c8ec21e7972471003ac165d072'''.</accordion> | ||
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Revision as of 22:42, 3 October 2019
of fluorescent reporters
ShuttleTracker can detect stained cell nuclei, generate corresponding annular perinuclear extensions, quantify geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking. Parameters of the image processing algorithms can be changed manually and the effects of these changes can be seen nearly immediately overlaid on currently displayed microscopic images. A key capability of ShuttleTracker is that nuclear contours and tracks can be generated automatically and then corrected manually. The tool is scriptable.
The latest ShuttleTracker version is 1.3.0 (September 2019).
Stand-alone binary executables for Windows and Mac
- Windows 64-bit installer: shuttletracker-1.3.0-x86_win64-setup.exe
SECURITY: The downloadable installer is not signed with a certificate (so in Windows parlance it comes from an "unknown publisher"); however, its integrity can be checked manually in command line using a Windows pre-installed utility:
- macOS application bundle (zipped "app"): shuttletracker-1.3.0-x86_64-darwin17.zip
SECURITY: MD5 sum of the downloadable ZIP archive can be checked in Terminal:
Containers for Linux
- A docker-based recipe for a Singularity container: shuttletracker-1.3.0-singularity.recipe
sudo singularity build --sandbox st shuttletracker-1.3.0-singularity.recipe
LAUNCHING the simulator within a container (in terminal):
singularity exec --writable st /opt/local/bin/ShuttleTracker
Source code
ShuttleTracker source code is distributed under GNU GPL v3.0.
- C++ source code: shuttletracker-1.3.0-source.tar.gz
tar xfz shuttletracker-1.3.0-source.tar.gz cd shuttletracker-1.3.0-source mkdir build && cd build cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/ make -j4 && make install
Documentation
- User's manual: shuttletracker-1.3.0-manual.pdf
- Step-by-step tutorial: TODO
and associated input images: March26_WellB_Pos09.zip (~1.3 GB)
Contact
The lead software developer is Marek Kochańczyk. For both user's and developer's queries please use the following e-mail address: shuttletracker.software@gmail.com