ShuttleTracker: Difference between revisions

Revision as of 23:17, 19 November 2018

An interactive tool for analyzing nucleocytoplasmic shuttling
of fluorescent reporters in living cells

ShuttleTracker can detect stained cell nuclei, generate corresponding annular perinuclear extensions, measure geometric and photometric properties of detected objects, and perform frame-to-frame nuclei tracking. Parameters of the underlying 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.

Example session

Downloads

ShuttleTracker is distributed under GNU GPL v3.0.
The latest ShuttleTracker version is 1.0.0.

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:

 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

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.

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:

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:

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):

 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

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

@@ Line 10: / Line 10: @@
 of ShuttleTracker is that nuclear contours and tracks can be generated
 automatically and then corrected manually.
-</div></div><br/>
+</div></div>
+<br/><br/>
 == Example session  ==
@@ Line 21: / Line 22: @@
-====Source code====
+==Source code==
 * C++ source code: &nbsp; [{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-source.tar.gz shuttletracker-1.0.0-source.tar.gz]
 <accordion parent="accordion" heading="How to compile">Compilation on Linux, Mac, and Windows is managed by [http://www.cmake.org/ CMake], which is expected to be used in the standard way:
@@ Line 33: / Line 34: @@
 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/>
-====Stand-alone executables====
+====Stand-alone binary executables====
 * Mac application bundle (zipped "app"): &nbsp; [{{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:&nbsp; 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:&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-1.0.0-x86_64-darwin16.zip is TODO</accordion>
@@ Line 41: / Line 42: @@
 ====Containers====
 * A docker-based recipe for a Singularity container: &nbsp;[{{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 build shuttletracker.simg shuttletracker-1.0.0-singularity.recipe
-   singularity exec shuttletracker-1.0.0.simg /opt/local/bin/ShuttleTracker</span></div></accordion>
+</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/>
 ====Documentation====