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EMBL BioImage Data Analysis

EuBIAS

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Timeline of @cmci_

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RT @albertcardona: Estimating the number of users of an image processing tool, using various data, educated guesses from tool writers, and…
About 1 day, 19 hours ago by: Kota Miura (@cmci_)

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Proud to see a copy in the hand of the original author! https://t.co/jxhw5svukk
About 3 days, 5 hours ago by: Kota Miura (@cmci_)

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... in fact, the @haesleinhuepf contribution is not an image data set but a set of IJ macros.
About 3 weeks, 4 days ago by: Kota Miura (@cmci_)

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Addition of three image data to the NEUBIAS community @ ZENODO. Thanks to the contributors! @_pm_lab… https://t.co/s42KbYlcNB
About 3 weeks, 4 days ago by: Kota Miura (@cmci_)

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RT @petebankhead: Calling all @QuPath users, we need your help! Please complete our survey to help us understand your needs & support our f…
About 3 weeks, 6 days ago by: Kota Miura (@cmci_)

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RT @JCellBiol: In this Viewpoint, @samjlord @KatrinaVelle @MullinsLab & @FritzLaylin propose a method to better display #reproducibility in…
About 1 month ago by: Kota Miura (@cmci_)
blogtng:blogtop
Algorithm Document FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R added 201904 Freiburg bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin




CMCI weblog

Server ImageJ Launcher

For easy access to use EMBL cluster for calculation using ImageJ, I tested using Jsch, a pure SSH2 implementation in Java (http://www.jcraft.com/jsch).

I made a ImageJ launcher that runs server-side ImageJ on local desktop (see GitHub repository ServerIJ). X should be ready for hosting the GUI. For further development, interface will be more boring as only some fields to input name of shell script and some options (path name to image files, macro or scripts) will be what you will see.

ELMI meeting 2011

This year, the meeting took place in southern Greece, Alexandroupolice, a small city with population of app. 60k. I list some talks related to image processing and analysis and some posters (might edit more afterward).

  • Erik Meijering (UMC Rotterdam) “Advances in tracking biological dynamics: from molecules to organisms” Comprehensive overview of recent tracking techniques. Erik showed a slide of a table showing a long list of available tracking software which will be in his paper coming to be published. Question still remains, if there could be “final algorithm” for all tracking.
  • Jason Sweldow (U. Dundee) “Using quantitative trajectory phenotyping to study the control of kinetochore dynamics during mitosis” Using auto- and cross correlation analysis to study the movement of sister kinetochores. 40 or so time points / 7.5 minutes per time point was required for analysis. Neat way to analyze kinetochore.
  • Christian Conrad (EMBL Heidelberg) “Micropilot - Automation of F-techniques for systems biology” Recursive system that enables complex analysis with high-throughput microscopy. FRAP analyss in such autoamtic way should be pretty effecient. I thought of some radically different way of time point sampling not from individual, but from population. Time coding > Population coding.
  • Gabor Csucs (ETH) “HCIP - workflow based Framework for Biological Image Processing using KNIME platform” KNIME is based on Eclipse framework and affords a user-friendly interface IDE, and this is now integrated with ImageJ including its plugins. Might be good for beginner entry points, who wants to combine functionality of several different analysis related software (though I have not tested yet).
  • Zoi Lygerou (U. Patras) “Stochasitc hybrid model of single molecule movement within cells permits insight into DNA replication silencing” Quite in a line of previous works done by Adriaan Houtsmuller and Ivo Sbalzarini. How they incorporated ODE with particle simulation is interesting, but was not presented.
  • Sebastian Tosi (CRG Barcelona) “Whole Organ and Tumor, Imaging and Analysis with Lightsheet Fluorescence Microscopy” Massive reconstruction of volume by combining Fiji and Imaris.
  • Iliana Kesisova (DU. Thrace) “Tripolins: Novel Aurora Kinase Inhibitors as Tools for Studying Mitosis” Was told that she worked with my ImageJ textbook so a special mention here!
  • M.A. Rapsomaniki, Presented by Zoi (U. Patras) “FRAPanalyzer: A Versatile Tool for Quantitative and Qualitative analysis of FRAP data” I was told that the idea is based on the Igor Frap Analyzer, migrated to the Matlab. Respect for another migration of my software. I think I need to publish all the implemented concepts I did with the software somewhere… Maybe this could be well compared with another version from Luxemburg.
  • Tania Patino “Identification and quantification of microparticle internalization in non-phagocytic cells by CSLM” I used to use PEI for enhance cell spreading on glass surface but here, it seems that PEI enhances internalization of micro-particle. I did not know this effect.
  • M. Del Cabo, Presented by Monica Roldan (UA Barcelobna) “ImageJ Automated Macro for the quantification of fat globules from a traditional catalan cheese from CSLM images” Quite facinating title and pictures, but more than that I was told that this is a product of our course we did in Barcelona in March (according to Julien Colombelli).

testing Groovy - ImageJ

There is a new ImageJ plugin that allows you to fo scripting with Groovy.

ij-Groovy
http://ij-plugins.sourceforge.net/plugins/groovy/tutorials.html#RecordingScripts

so I became interested in how it would be like using it. GroovyConsole seems to be an handy Editor, so instead of installing the plugin to ImageJ, I made a trial to use ImageJ as a libray, accessing directly from Groovy. It was pretty simple to do this task, but I note down how I installed mainly because I will forget what I did.

1. Go to the groovy site, and download the zipped binary.
http://groovy.codehaus.org/Download

I downloaded Groovy 1.7.8 and unzipped the folder groovy-1.7.8 under C:\dev.

2. Add path C:\dev\groovy-1.7.8 as a new environmental variable “GROOVY_HOME” .

3. Add path %GROOVY_HOME%\bin to the system path.

4. Launch the console by clicking %GROOVY_HOME%\bin\GroovyConsole.bat

5. set path to ij.jar by [Script > Add Jar to Classpath]

Following is the code I tested, which worked fine without opening ImageJ main menu.

import ij.*

imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/gel.gif");
IJ.log(imp.getDimensions()[0].toString());
imp.show();

Running this code, an image window pops sup and also the width of the image is printed in the output field of the console. IJ.log command which normally should print out the string argument in log window seems to be diverted to the console output.
Interpreter runs with a speed comparable to Javascript and Jython running with ImageJ jar.

Good point about this console is that referencing to a jar file could be easily be done, by [scripts > add jar to classpath] This affords a good simple interface for test assembling several Java libraries.

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Weblog Archive

blogtng/blogtop.txt · Last modified: 2021/01/25 02:26 by kota