ShuttleTracker: Difference between revisions
From Laboratory of Modeling in Biology and Medicine
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===Containers for Linux=== | ===Containers for Linux=== | ||
* | * Docker container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.0.Dockerfile shuttletracker-1.5.0.Dockerfile]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | ||
docker build . -f shuttletracker-1.5.0.Dockerfile --tag st-container | docker build . -f shuttletracker-1.5.0.Dockerfile --tag st-container | ||
</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | </span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | ||
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xhost +local:docker | xhost +local:docker | ||
</span></div></accordion> | </span></div></accordion> | ||
* | * Singularity container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.0.recipe shuttletracker-1.5.0.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | ||
sudo singularity build --sandbox st shuttletracker-1.5.0.recipe | sudo singularity build --sandbox st shuttletracker-1.5.0.recipe | ||
</span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | </span></div><br/>LAUNCHING the GUI app within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | ||
Revision as of 11:52, 24 May 2021
An interactive tool for analyzing nucleocytoplasmic shuttling
of fluorescent reporters
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 1.5.0 (May 2021).
Documentation
- User's manual: shuttletracker-1.5.0-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-1.5.0-x86_win64-setup.exe
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:
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-1.5.0-x86_win64-setup.exe is 23720f35399d4ae61f772c49b07826d6.- macOS application bundle (zipped "app"): shuttletracker-1.4.5-x86_64-darwin17.zip
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:
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-1.5.0.Dockerfile
BUILDING a container (in terminal):
LAUNCHING the GUI app within a container (in terminal):
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:
docker build . -f shuttletracker-1.5.0.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-1.5.0.recipe
BUILDING a container (in terminal):
LAUNCHING the GUI app within a container (in terminal):
sudo singularity build --sandbox st shuttletracker-1.5.0.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-1.5.0-source.tar.gz
Compilation on Linux, macOS, and Windows is managed by CMake, which is expected to be used in the standard way:
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.
tar xfz shuttletracker-1.5.0-source.tar.gz cd shuttletracker-1.5.0-source mkdir build && cd build cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/ make -j4 && make install
Published applications
- 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.
