ShuttleTracker: Difference between revisions
From Laboratory of Modeling in Biology and Medicine
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The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.0.0'''. | The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.0.0'''. | ||
====Stand-alone binary executables==== | |||
* Mac application bundle (zipped "app"): [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-x86_64-darwin16.zip shuttletracker-1.0.0-x86_64-darwin16.zip]<accordion parent="accordion" heading="How to verify and run">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).<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-1.0.0-x86_64-darwin16.zip is TODO</accordion> | |||
* Windows 64-bit installer: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-x86_win64-setup.exe shuttletracker-1.0.0-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-1.0.0-x86_win64-setup.exe is TODO<br/></accordion> | |||
<br/> | |||
====Containers==== | |||
* A docker-based recipe for a Singularity container: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-singularity.recipe shuttletracker-1.0.0-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-1.0.0-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;"> | |||
singularity exec shuttletracker-1.0.0.simg /opt/local/bin/ShuttleTracker | |||
</span></div></accordion> | |||
<br/> | |||
====Source code==== | ====Source code==== | ||
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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.</accordion> | 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.</accordion> | ||
<br/> | <br/> | ||
====Documentation==== | ====Documentation==== | ||
* User's manual: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-manual.pdf shuttletracker-1.0.0-manual.pdf] | * User's manual: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-manual.pdf shuttletracker-1.0.0-manual.pdf] | ||
<br/> | <br/> | ||
====Example images==== | ====Example images==== | ||
* An archive with example S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> files: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-examples.zip shuttletracker-1.0.0-examples.zip] | * An archive with example S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> files: [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-examples.zip shuttletracker-1.0.0-examples.zip] | ||
Revision as of 13:39, 29 November 2018
An interactive tool for analyzing nucleocytoplasmic shuttling
of fluorescent reporters in living cells
of fluorescent reporters in living cells
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. Automation is enabled by scripting.
Example session
Downloads
ShuttleTracker is distributed under GNU GPL v3.0.
The latest ShuttleTracker version is 1.0.0.
Stand-alone binary executables
- Mac application bundle (zipped "app"): shuttletracker-1.0.0-x86_64-darwin16.zip
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:
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- Windows 64-bit installer: shuttletracker-1.0.0-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-1.0.0-x86_win64-setup.exe is TODO
Containers
- A docker-based recipe for a Singularity container: shuttletracker-1.0.0-singularity.recipe
BUILDING a container (in terminal):
LAUNCHING the simulator within 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
Source code
- C++ source code: shuttletracker-1.0.0-source.tar.gz
Compilation on Linux, Mac, 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-1.0.0-manual.pdf
Example images
- An archive with example ShuttleTracker files: shuttletracker-1.0.0-examples.zip
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
