ShuttleTracker: Difference between revisions
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<div align="center">'''An interactive tool for analyzing nucleocytoplasmic shuttling<br/> of fluorescent reporters<!-- in living cells-->'''</div><br /> | <div align="center">'''An interactive tool for analyzing nucleocytoplasmic shuttling<br/> of fluorescent reporters<!-- in living cells-->'''</div><br /> | ||
<div align="center"> | <div align="center"> | ||
[[Image:ShuttleTracker_montage.png|link={{SERVER}}/images/7/7e/ShuttleTracker_montage.png|500px]] | |||
<div align="left" style="width:520px"> | <div align="left" style="width:520px"> | ||
S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> 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. <br/><br/> | S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> 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. <br/><br/> | ||
The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1. | The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.5.3''' (February 2023). | ||
</div></div> | </div></div> | ||
<br/><br/> | <br/><br/> | ||
===Documentation=== | |||
* User's manual: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-manual.pdf shuttletracker-1.5.3-manual.pdf]<br style="line-height: 100%; margin-bottom:14px"> | |||
* Tutorial and overview: [{{SERVER}}/software/shuttletracker/release/previous/shuttletracker-1.3.0-tutorial.pdf shuttletracker-1.3.0-tutorial.pdf]<!--<span style="background:yellow"> ''' TODO ''' </span>--><br style="line-height: 100%; margin-bottom:6px">+ example input images: [{{SERVER}}/software/shuttletracker/tutorial/March26_WellB_Pos09.zip March26_WellB_Pos09.zip] (~1.3 GB)<br style="line-height: 100%; margin-bottom:6px">+ example output from tracking analysis: [{{SERVER}}/software/shuttletracker/tutorial/March26_WellB_Pos09.html March26_WellB_Pos09.html] | |||
<br/> | |||
===Stand-alone binary executables for Windows and Mac=== | ===Stand-alone binary executables for Windows and Mac=== | ||
* Windows 64-bit installer: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * Windows 64-bit installer: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-x86_win64-setup.exe shuttletracker-1.5.3-x86_win64-setup.exe]<div class="accordion" id="accordion-win"><accordion parent="accordion-win" heading="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.<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-1.5.3-x86_win64-setup.exe is '''d6a87dec0b6167ae12833821d6d8a208'''.<br/></accordion></div> | ||
* macOS application bundle (zipped "app"): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * macOS application bundle (zipped "app", outdated): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.4.5-x86_64-darwin17.zip shuttletracker-1.4.5-x86_64-darwin17.zip]<div class="accordion" id="accordion-mac"><accordion parent="accordion-mac" 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-1.4.5-x86_64-darwin17.zip is '''68ed03597b5e43e02ceace2e3530ce38'''.</accordion></div> | ||
<br/> | <br/> | ||
===Containers for Linux=== | ===Containers for Linux=== | ||
* | * Docker container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3.Dockerfile shuttletracker-1.5.3.Dockerfile]<div class="accordion" id="accordion-docker"><accordion parent="accordion-docker" 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;"> | ||
singularity build | docker build . -f shuttletracker-1.5.3.Dockerfile --tag st-container | ||
</span></div><br/>LAUNCHING the | </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;"> | ||
singularity exec | docker run -e DISPLAY --net=host st-container | ||
</span></div></accordion> | </span></div><br/>You will likely want to specify a filesystem location with images using docker run's flag <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">-v</span>. If the app fails to connect to the windows server, you may need to grant permission as follows: <div align="left"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | ||
<br/> | xhost +local:docker | ||
</span></div></accordion></div> | |||
* Singularity container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3.recipe shuttletracker-1.5.3.recipe]<div class="accordion" id="accordion-singularity"><accordion parent="accordion-singularity" 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-1.5.3.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;"> | |||
singularity exec --writable st /opt/local/bin/ShuttleTracker | |||
</span></div></accordion><div><br/> | |||
===Source code=== | ===Source code=== | ||
S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> source code is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/> | S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> source code is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/> | ||
* C++ source code: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * C++ source code: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.5.3-source.tar.gz shuttletracker-1.5.3-source.tar.gz] | ||
<accordion parent="accordion" heading="How to compile">Compilation on Linux, macOS, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way: | <div class="accordion" id="accordion-sourcecode"><accordion parent="accordion-sourcecode" heading="How to compile">Compilation on Linux, macOS, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way: | ||
<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | <div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;"> | ||
tar xfz shuttletracker- | tar xfz shuttletracker-1.5.3-source.tar.gz | ||
cd shuttletracker- | cd shuttletracker-1.5.3-source | ||
mkdir build && cd build | mkdir build && cd build | ||
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/ | cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/ | ||
make -j4 && make install | make -j4 && make install | ||
</span></div> | </span></div> | ||
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.<br/></accordion> | 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.<br/></accordion></div> | ||
<br/> | <br/> | ||
=== | <!-- | ||
* | ===References=== | ||
* | ====Primary citation==== | ||
< | * <span class="pmbm">Kochańczyk M</span>. '''ShuttleTracker: an interactive tool for analysing nucleocytoplasmic shuttling of fluorescent reporters''' (''submitted'')<br style="margin-bottom:12px">--> | ||
===Applications=== | |||
* <span class="pmbm">Korwek Z</span>, <i>et al</i>. '''Nonself RNA rewires IFNβ signaling: A mathematical model of the innate immune response''', ''Science Signaling'' (accepted) [https://doi.org/10.1101/2022.01.30.478391 bioRxiv]<br style="line-height: 100%; margin-bottom:12px"> | |||
* <span class="pmbm">Grabowski F</span>, <i>et al</i>. '''Antagonism between viral infection and innate immunity at the single-cell level''', ''PLOS Pathogens'' <u>19</u>:e1011597 (2023) [https://pubmed.ncbi.nlm.nih.gov/37669278 PubMed] [https://doi.org/10.1371/journal.ppat.1011597 CrossRef]<br style="line-height: 100%; margin-bottom:12px"> | |||
* <span class="author">Czerkies M</span>, <i>et al</i>. '''Respiratory syncytial virus protects bystander cells against influenza A virus infection by triggering secretion of type I and type III interferons''', ''Journal of Virology'' <u>96</u>:22 e01341-22 (2022) [https://doi.org/10.1128/jvi.01341-22 CrossRef] [https://doi.org/10.1101/2021.10.11.463877 bioRxiv]<br style="line-height: 100%; margin-bottom:12px"> | |||
* <span class="pmbm">Czerkies M</span>, <i>et al</i>. '''Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways''', ''Nature Communications'' <u>9</u>:493 (2018) [http://www.ncbi.nlm.nih.gov/pubmed/29402958 PubMed] [http://dx.doi.org/10.1038/s41467-017-02640-8 CrossRef]<br style="line-height: 100%; margin-bottom:12px"> | |||
* <span class="pmbm">Tudelska K</span>, <i>et al</i>. '''Information processing in the NF-κB pathway''', ''Scientific Reports'' <u>7</u>:15926 (2017) [http://www.ncbi.nlm.nih.gov/pubmed/29162874 PubMed] [http://doi.org/10.1038/s41598-017-16166-y CrossRef] | |||
<br/> | |||
===Contact=== | ===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 | 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. | ||
<br/><br/> | <br/><br/> | ||
Latest revision as of 19:24, 7 November 2023
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
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", outdated): shuttletracker-1.4.5-x86_64-darwin17.zip
SECURITY: MD5 sum of the downloadable ZIP archive can be checked in Terminal:
Containers for Linux
- Docker container: shuttletracker-1.5.3.Dockerfile
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
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
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
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
- 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.