ShuttleTracker: Difference between revisions

Revision as of 23:13, 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 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 2: / Line 2: @@
 <div align="center">
 <div align="left" style="width:520px">
-ShuttleTracker can detect stained cell nuclei, generate corresponding
+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, measure geometric and photometric properties of detected
 objects, and perform frame-to-frame nuclei tracking.&nbsp; Parameters of
@@ Line 11: / Line 11: @@
 automatically and then corrected manually.
 </div></div><br/>
-<!--
+== Example session  ==
+<br/><br/>
 == Downloads ==
-* [http://pmbm.ippt.pan.pl/software/shuttletracker/release/shuttletracker-v1.0.0.tar.gz ShuttleTracker 1.0.0 source code]
-* [http://pmbm.ippt.pan.pl/software/shuttletracker/tutorial/shuttletracker-1.0.0-tutorial.zip Example input images] (~? GB)
+S<span style="font-variant:small-caps">huttle</span>T<span style="font-variant:small-caps">racker</span> is distributed under [http://www.gnu.org/licenses/gpl-3.0.html GNU GPL v3.0].<br/>
--->
+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'''.
+====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:
+<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">
+  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
+</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.</accordion>
+<br/>
+====Stand-alone 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,Inconsolatam,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: &nbsp; [{{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:&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,Inconsolatam,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: &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,Inconsolatam,monospace;">singularity exec shuttletracker-1.0.0.simg /opt/local/bin/ShuttleTracker</span></div></accordion>
+<br/>
+====Documentation====
+* User's manual: &nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-manual.pdf shuttletracker-1.0.0-manual.pdf]
+<br/>
+====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: &nbsp;[{{SERVER}}/software/shuttletracker/release/shuttletracker-1.0.0-examples.zip shuttletracker-1.0.0-examples.zip]
+<br/><br/>
 == Contact ==