Difference between revisions of "Team:Slovenia/Software"

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<h2><span id="intro" class="section"> &nbsp; </span> Software </h2>
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<h2><span id="intro" class="section"> &nbsp; </span></h2>
 
<p>
 
<p>
 
CaPTURE software was developed by the Slovenian 2016 iGEM team with an aim to analyze the calcium influx into mammalian cells upon ultrasound stimulation of mechanosensitive channels detected by the fluorescence microscopy. CaPTURE analyses the digital images from the confocal microscope to detect the cellular response to stimulation by change of the fluorescence. Software calculates the ratio of the fluorescence in two channels and it automatically scans for the response regions using the sliding window technique and provides the temporal response of cells. Track of each cell can be monitored or average calculated and different threshold and selection criteria can be set. The software was prepared for our Sonicell project, but it can be used for virtually any time dependent images the synthetic biology community.  
 
CaPTURE software was developed by the Slovenian 2016 iGEM team with an aim to analyze the calcium influx into mammalian cells upon ultrasound stimulation of mechanosensitive channels detected by the fluorescence microscopy. CaPTURE analyses the digital images from the confocal microscope to detect the cellular response to stimulation by change of the fluorescence. Software calculates the ratio of the fluorescence in two channels and it automatically scans for the response regions using the sliding window technique and provides the temporal response of cells. Track of each cell can be monitored or average calculated and different threshold and selection criteria can be set. The software was prepared for our Sonicell project, but it can be used for virtually any time dependent images the synthetic biology community.  
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<h2><span id="req" class="section"> &nbsp; </span> System requirements </h2>
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<h3><span id="req" class="section"> &nbsp; </span> System requirements </h3>
 
<p>CaPTURE runs on any system equipped with the Java Virtual Machine (1.7 or newer), which can be
 
<p>CaPTURE runs on any system equipped with the Java Virtual Machine (1.7 or newer), which can be
 
downloaded at no
 
downloaded at no
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<h2><span id="install"  class="section"> &nbsp; </span> Installing and running </h2>
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<h3><span id="install"  class="section"> &nbsp; </span> Installing and running </h3>
 
<p> Download the <a href="//2016.igem.org/wiki/images/8/8f/T--Slovenia--CaPTURE.zip">CaPTURE folder</a>
 
<p> Download the <a href="//2016.igem.org/wiki/images/8/8f/T--Slovenia--CaPTURE.zip">CaPTURE folder</a>
 
and unzip it. CaPTURE is also available on <a href="//github.com/zigapusnik/CaPTURE">GitHub</a>. The simplest way to run the program is by double
 
and unzip it. CaPTURE is also available on <a href="//github.com/zigapusnik/CaPTURE">GitHub</a>. The simplest way to run the program is by double
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<h2><span id="build"  class="section"> &nbsp; </span> Building from source </h2>
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<h3><span id="build"  class="section"> &nbsp; </span> Building from source </h3>
 
<p>
 
<p>
 
To build the application from source, follow the given steps: </p>
 
To build the application from source, follow the given steps: </p>
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<h2><span id="faq"  class="section">&nbsp; </span> FAQ</h2>
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<h3><span id="faq"  class="section">&nbsp; </span> FAQ</h3>
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<h3> I tried to open a file, but CaPTURE froze during the processing. What should I
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<h5> I tried to open a file, but CaPTURE froze during the processing. What should I
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do? </h3>
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do? </h5>
 
<p> Most likely your JVM ran out of memory. While it is not possible to addres more than 4GB with 32
 
<p> Most likely your JVM ran out of memory. While it is not possible to addres more than 4GB with 32
 
bit Java, 64 bit version is prefered. It is also possible to increase the maximum heap size
 
bit Java, 64 bit version is prefered. It is also possible to increase the maximum heap size
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<h3> I want to open several files at the same time. How to do it? </h3>
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<h5> I want to open several files at the same time. How to do it? </h5>
 
<p> Currently only one file can be loaded. You can, however, open a new instance of CaPTURE and
 
<p> Currently only one file can be loaded. You can, however, open a new instance of CaPTURE and
 
analyze the second file in it.
 
analyze the second file in it.
 
</p>
 
</p>
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<h3> I cannot open other microscopic file formats. Are other formats not supported? </h3>
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<h5> I cannot open other microscopic file formats. Are other formats not supported? </h5>
 
<p> Currently only .lif format is supported, however in the future CaPTURE will support other
 
<p> Currently only .lif format is supported, however in the future CaPTURE will support other
 
microscopic image formats.
 
microscopic image formats.
 
</p>
 
</p>
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<h3 style="white-space:normal"> I tried to compile the source using my OpenJDK implementation, but
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<h5 style="white-space:normal"> I tried to compile the source using my OpenJDK implementation, but
 
got the following error "TimeLineJForm.java:37: error: package javafx.stage does not
 
got the following error "TimeLineJForm.java:37: error: package javafx.stage does not
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exist". </h3>
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exist". </h5>
 
<p><a href="//wiki.openjdk.java.net/display/OpenJFX/Main">OpenJFX</a> is needed to compile the
 
<p><a href="//wiki.openjdk.java.net/display/OpenJFX/Main">OpenJFX</a> is needed to compile the
 
source code. For many platforms you can simply install (or update) JDK 8.
 
source code. For many platforms you can simply install (or update) JDK 8.

Revision as of 21:03, 16 October 2016

Software

Logic CaPTURE System requirements Installing and running Building from source FAQ Hardware

 

CaPTURE software was developed by the Slovenian 2016 iGEM team with an aim to analyze the calcium influx into mammalian cells upon ultrasound stimulation of mechanosensitive channels detected by the fluorescence microscopy. CaPTURE analyses the digital images from the confocal microscope to detect the cellular response to stimulation by change of the fluorescence. Software calculates the ratio of the fluorescence in two channels and it automatically scans for the response regions using the sliding window technique and provides the temporal response of cells. Track of each cell can be monitored or average calculated and different threshold and selection criteria can be set. The software was prepared for our Sonicell project, but it can be used for virtually any time dependent images the synthetic biology community.

  System requirements

CaPTURE runs on any system equipped with the Java Virtual Machine (1.7 or newer), which can be downloaded at no cost from Oracle.

  Installing and running

Download the CaPTURE folder and unzip it. CaPTURE is also available on GitHub. The simplest way to run the program is by double clicking on the CaPTURE.jar file, however, it might not work on some systems. Alternatively, execute the program from the command line using the following command:

java -jar CaPTURE.jar

To run the application from the JAR file that is in another directory, you must specify the path of that directory:

java -jar path/CaPTURE.jar

Note that on Windows the forward slash as the directory separator should be replaced with a backslash. To test the software you can download the example .lif file. Extract the file and open it with CaPTURE.

  Building from source

To build the application from source, follow the given steps:

  • Download CaPTURE and unzip it.
  • Change the working directory to unzipped CaPTURE folder.
  • Then compile .java source files to executable .class files.
  • Copy bioformats_package.jar and icon.png resource file from the src directory in the scanPackage directory that was created during the compilation.
  • Create a single java archive file from multiple .class files.
  • Then you can start the program.

Linux & OS X:

cd CaPTURE
javac -d . -cp src/bioformats_package.jar src/*.java
cp src/icon.png scanPackage
jar cfm CaPTURE.jar MANIFEST.MF scanPackage
java -jar CaPTURE.jar

Windows:

cd CaPTURE
javac -d . -cp src\bioformats_package.jar src\*.java
robocopy src scanPackage icon.png
jar cfm CaPTURE.jar MANIFEST.MF scanPackage
java -jar CaPTURE.jar

  FAQ

I tried to open a file, but CaPTURE froze during the processing. What should I do?

Most likely your JVM ran out of memory. While it is not possible to addres more than 4GB with 32 bit Java, 64 bit version is prefered. It is also possible to increase the maximum heap size using the -Xmx switch. For maximum heap size of 1024 MB the following command should be executed from the command line:

java -Xmx1024m -jar CaPTURE.jar
I want to open several files at the same time. How to do it?

Currently only one file can be loaded. You can, however, open a new instance of CaPTURE and analyze the second file in it.

I cannot open other microscopic file formats. Are other formats not supported?

Currently only .lif format is supported, however in the future CaPTURE will support other microscopic image formats.

I tried to compile the source using my OpenJDK implementation, but got the following error "TimeLineJForm.java:37: error: package javafx.stage does not exist".

OpenJFX is needed to compile the source code. For many platforms you can simply install (or update) JDK 8.