ShuttleTracker: Difference between revisions

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* Windows 64-bit installer: &nbsp; [{{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:&nbsp; This software was built with MSVC14 on Windows&nbsp;10, and tested on Windows&nbsp;10 and Windows&nbsp;8. An installer of Microsoft Visual C++ 2017 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:&nbsp; 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: &nbsp; [{{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:&nbsp; This software was built with MSVC14 on Windows&nbsp;10, and tested on Windows&nbsp;10 and Windows&nbsp;8. An installer of Microsoft Visual C++ 2017 Redistributable (required runtime libraries) is contained in the ShuttleTracker installer.<br/><br/>SECURITY:&nbsp; 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"): &nbsp;[{{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:&nbsp; 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:&nbsp; 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 '''b3ad9b3bb4d3e1dc812ec0b09e0e4d96'''.</accordion>
* macOS application bundle (zipped "app"): &nbsp;[{{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:&nbsp; 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:&nbsp; 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

An interactive tool for analyzing nucleocytoplasmic shuttling
of fluorescent reporters


ShuttleTracker montage.png

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

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.

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:
certUtil -hashfile path_to_installer MD5
MD5 sum of untainted shuttletracker-1.3.0-x86_win64-setup.exe is 18d220e5d499239a50b75da2df68a05d.

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.

SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:
md5 path_to_zip
MD5 sum of untainted shuttletracker-1.3.0-x86_64-darwin17.zip is 7cffa9c8ec21e7972471003ac165d072.


Containers for Linux

BUILDING a container (in terminal):
 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.

Compilation on Linux, macOS, and Windows is managed by CMake, which is expected to be used in the standard way:
 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 
More detailed instructions are provided in file COMPILING.md in the source code package. You may also have a look at how the build process is automated in a Singularity container recipe distributed in source code distribution subdirectory distrib/singularity.


Documentation



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