ShuttleTracker

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An interactive tool for analyzing nucleocytoplasmic shuttling
of fluorescent reporters in living cells


ShuttleTracker can detect stained cell nuclei, generate corresponding annular perinuclear extensions, measure geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking.  Parameters of the underlying 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.


Example session



Downloads

ShuttleTracker is distributed under GNU GPL v3.0.
The latest ShuttleTracker version is 1.0.0.


Source code

Compilation on Linux, Mac, and Windows is managed by CMake, which is expected to be used in the standard way:
 tar xfz shuttletracker-VERSION-source.tar.gz
 cd shuttletracker-VERSION-source
 mkdir build && cd build
 cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/
 make -j4 && make install 
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.


Stand-alone executables

COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.12 (Sierra). It is likely incompatible with previous Mac operating system releases. It has been confirmed to work on macOS 10.13 (High Sierra).

SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:
md5 path_to_zip
MD5 sum of untainted shuttletracker-1.0.0-x86_64-darwin16.zip is TODO

COMPATIBILITY:  This software was built with MSVC14 on Windows 10, and tested on Windows 10 and Windows 8.

SECURITY:  The downloadable installer is not signed with a certificate (so in windows terms it comes from an "unknown publisher") but 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-1.0.0-x86_win64-setup.exe is TODO


Containers

BUILDING a container (in terminal):
singularity build shuttletracker.simg shuttletracker-1.0.0-singularity.recipe

LAUNCHING the simulator within a container (in terminal):
singularity exec shuttletracker-1.0.0.simg /opt/local/bin/ShuttleTracker


Documentation


Example images




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