ShuttleTracker: Difference between revisions
From Laboratory of Modeling in Biology and Medicine
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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 '''1.2.0'''. | ||
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===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-1.2.0-x86_win64-setup.exe shuttletracker-1.2.0-x86_win64-setup.exe]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY: This software was built with MSVC14 on Windows 10, and tested on Windows 10 and Windows 8.<br/><br/>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:<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-1.2.0-x86_win64-setup.exe is '''TODO'''.<br/></accordion> | ||
* macOS application bundle (zipped "app"): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * macOS application bundle (zipped "app"): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-x86_64-darwin17.zip shuttletracker-1.2.0-x86_64-darwin17.zip]<accordion parent="accordion" 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-1.2.0-x86_64-darwin17.zip is '''TODO'''.</accordion> | ||
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===Containers for Linux=== | ===Containers for Linux=== | ||
* A docker-based recipe for a Singularity container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * A docker-based recipe for a Singularity container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-singularity.recipe shuttletracker-1.2.0-singularity.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;"> | ||
singularity build shuttletracker.simg shuttletracker-1. | singularity build shuttletracker.simg shuttletracker-1.2.0-singularity.recipe | ||
</span></div><br/>LAUNCHING the simulator 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 simulator 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 shuttletracker-1. | singularity exec shuttletracker-1.2.0.simg /opt/local/bin/ShuttleTracker | ||
</span></div></accordion> | </span></div></accordion> | ||
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===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-1.2.0-source.tar.gz shuttletracker-1.2.0-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: | <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 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;"> | ||
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===Documentation=== | ===Documentation=== | ||
* User's manual: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * User's manual: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-manual.pdf shuttletracker-1.2.0-manual.pdf] | ||
* An archive with tutorial instructions and images: <span style="background:yellow"> ''' TODO ''' </span><!-- [{{SERVER}}/software/shuttletracker/release/shuttletracker-1. | * An archive with tutorial instructions and images: <span style="background:yellow"> ''' TODO ''' </span><!-- [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-tutorial.zip shuttletracker-1.2.0-tutorial.zip]--> | ||
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Revision as of 22:14, 4 July 2019
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 1.2.0.
Stand-alone binary executables for Windows and Mac
- Windows 64-bit installer: shuttletracker-1.2.0-x86_win64-setup.exe
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:
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-1.2.0-x86_win64-setup.exe is TODO.- macOS application bundle (zipped "app"): shuttletracker-1.2.0-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-1.2.0-x86_64-darwin17.zip is TODO.
Containers for Linux
- A docker-based recipe for a Singularity container: shuttletracker-1.2.0-singularity.recipe
BUILDING a container (in terminal):
LAUNCHING the simulator within a container (in terminal):
singularity build shuttletracker.simg shuttletracker-1.2.0-singularity.recipe
LAUNCHING the simulator within a container (in terminal):
singularity exec shuttletracker-1.2.0.simg /opt/local/bin/ShuttleTracker
Source code
ShuttleTracker source code is distributed under GNU GPL v3.0.
- C++ source code: shuttletracker-1.2.0-source.tar.gz
Compilation on Linux, macOS, and Windows is managed by CMake, which is expected to be used in the standard way:
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.
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
Documentation
- User's manual: shuttletracker-1.2.0-manual.pdf
- An archive with tutorial instructions and images: TODO
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
