ShuttleTracker

An interactive tool for analyzing nucleocytoplasmic shuttling
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 1.5.3 (February 2023).

Documentation

• User's manual:  shuttletracker-1.5.3-manual.pdf
  
• Tutorial and overview:  shuttletracker-1.3.0-tutorial.pdf
  + example input images:  March26_WellB_Pos09.zip (~1.3 GB)
  + example output from tracking analysis:  March26_WellB_Pos09.html

Stand-alone binary executables for Windows and Mac

• Windows 64-bit installer:   shuttletracker-1.5.3-x86_win64-setup.exe

How to verify and run

COMPATIBILITY:  This software was built with MSVC 14.2 on Windows 10, and tested on Windows 10 and Windows 8. An installer of Microsoft Visual C++ 2019 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-1.5.3-x86_win64-setup.exe is d6a87dec0b6167ae12833821d6d8a208.

• macOS application bundle (zipped "app", outdated):  shuttletracker-1.4.5-x86_64-darwin17.zip

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.

SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:

md5 path_to_zip

MD5 sum of untainted shuttletracker-1.4.5-x86_64-darwin17.zip is 68ed03597b5e43e02ceace2e3530ce38.

Containers for Linux

• Docker container:  shuttletracker-1.5.3.Dockerfile

How to set up and run

BUILDING a container (in terminal):

 docker build .  -f shuttletracker-1.5.3.Dockerfile  --tag st-container

LAUNCHING the GUI app within a container (in terminal):

 docker run  -e DISPLAY  --net=host  st-container

You will likely want to specify a filesystem location with images using docker run's flag -v. If the app fails to connect to the windows server, you may need to grant permission as follows:

 xhost +local:docker

• Singularity container:  shuttletracker-1.5.3.recipe

How to set up and run

BUILDING a container (in terminal):

 sudo singularity build --sandbox st shuttletracker-1.5.3.recipe

LAUNCHING the GUI app 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-1.5.3-source.tar.gz

How to compile

Compilation on Linux, macOS, and Windows is managed by CMake, which is expected to be used in the standard way:

 tar xfz shuttletracker-1.5.3-source.tar.gz
 cd shuttletracker-1.5.3-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 the source code distribution subdirectory distrib/singularity.

Applications

• Korwek Z, et al. Nonself RNA rewires IFNβ signaling: A mathematical model of the innate immune response, Science Signaling (accepted) bioRxiv
  
• Grabowski F, et al. Antagonism between viral infection and innate immunity at the single-cell level, PLOS Pathogens 19:e1011597 (2023) PubMed CrossRef
  
• Czerkies M, et al. Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons, Journal of Virology 96:22 e01341-22 (2022) CrossRef bioRxiv
  
• Czerkies M, et al. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways, Nature Communications 9:493 (2018) PubMed CrossRef
  
• Tudelska K, et al. Information processing in the NF-κB pathway, Scientific Reports 7:15926 (2017) PubMed CrossRef

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.