ShuttleTracker: Difference between revisions

Revision as of 22:59, 29 September 2019

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 1.3.0.

Stand-alone binary executables for Windows and Mac

Windows 64-bit installer: TODO

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:

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"): TODO

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-1.2.0-x86_64-darwin17.zip is TODO .

Containers for Linux

A docker-based recipe for a Singularity container: shuttletracker-1.3.0-singularity.recipe

BUILDING a container (in terminal):

 singularity build shuttletracker.simg shuttletracker-1.3.0-singularity.recipe

LAUNCHING the simulator within a container (in terminal):

 singularity exec shuttletracker.simg /opt/local/bin/ShuttleTracker

Source code

ShuttleTracker source code is distributed under GNU GPL v3.0.

C++ source code: shuttletracker-1.3.0-source.tar.gz

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

 tar xfz shuttletracker-1.3.0-source.tar.gz
 cd shuttletracker-1.3.0-source
 mkdir build && cd build
 cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/
 make -j4 && make install

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.

Documentation

User's manual: shuttletracker-1.3.0-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

@@ Line 3: / Line 3: @@
 <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.&nbsp; 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.&nbsp; 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 '''1.2.0'''.
+The latest S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> version is '''1.3.0'''.
 </div></div>
 <br/><br/>
 ===Stand-alone binary executables for Windows and Mac===
-* Windows 64-bit installer: &nbsp; [{{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:&nbsp; This software was built with MSVC14 on Windows&nbsp;10, and tested on Windows&nbsp;10 and Windows&nbsp;8.<br/><br/>SECURITY:&nbsp; 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 '''730658ddc8a5951e1ed832a81a260b7a'''.<br/></accordion>
+* Windows 64-bit installer: &nbsp; <!--[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-x86_win64-setup.exe shuttletracker-1.2.0-x86_win64-setup.exe]--><span style="background:yellow">&nbsp;''' TODO '''&nbsp;</span><accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:&nbsp; This software was built with MSVC14 on Windows&nbsp;10, and tested on Windows&nbsp;10 and Windows&nbsp;8.<br/><br/>SECURITY:&nbsp; 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 <!--'''730658ddc8a5951e1ed832a81a260b7a'''--><span style="background:yellow">&nbsp;''' TODO '''&nbsp;</span>.<br/></accordion>
-* macOS application bundle (zipped "app"): &nbsp; [{{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:&nbsp; 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:&nbsp; 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 '''f5d2a5ebf81b72a6b8a521205df192e8'''.</accordion>
+* macOS application bundle (zipped "app"): &nbsp; <!--[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-x86_64-darwin17.zip shuttletracker-1.2.0-x86_64-darwin17.zip]--><span style="background:yellow">&nbsp;''' TODO '''&nbsp;</span><accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:&nbsp; 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:&nbsp; 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 <!--'''f5d2a5ebf81b72a6b8a521205df192e8'''--><span style="background:yellow">&nbsp;''' TODO '''&nbsp;</span>.</accordion>
 <br/>
 ===Containers for Linux===
-* A docker-based recipe for a Singularity container: &nbsp;[{{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;">
+* A docker-based recipe for a Singularity container: &nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-singularity.recipe shuttletracker-1.3.0-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-1.2.0-singularity.recipe
+   singularity build shuttletracker.simg shuttletracker-1.3.0-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.simg /opt/local/bin/ShuttleTracker
@@ Line 23: / Line 23: @@
 ===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/>
-* C++ source code: &nbsp; [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-source.tar.gz shuttletracker-1.2.0-source.tar.gz]
+* C++ source code: &nbsp; [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-source.tar.gz shuttletracker-1.3.0-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:
 <div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">
-   tar xfz shuttletracker-VERSION-source.tar.gz
+   tar xfz shuttletracker-1.3.0-source.tar.gz
-   cd shuttletracker-VERSION-source
+   cd shuttletracker-1.3.0-source
    mkdir build && cd build
    cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/local/
@@ Line 36: / Line 36: @@
 ===Documentation===
-* User's manual: &nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-manual.pdf shuttletracker-1.2.0-manual.pdf]
+* User's manual: &nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-manual.pdf shuttletracker-1.3.0-manual.pdf]
-* An archive with tutorial instructions and images: <span style="background:yellow">&nbsp;''' TODO '''&nbsp;</span><!--&nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.2.0-tutorial.zip shuttletracker-1.2.0-tutorial.zip]-->
+* An archive with tutorial instructions and images: <span style="background:yellow">&nbsp;''' TODO '''&nbsp;</span><!--&nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.3.0-tutorial.zip shuttletracker-1.3.0-tutorial.zip]-->
 <br/><br/>