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EMBL BioImage Data Analysis



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RT @florianjug: If you missed the webinar but are interested to have a look, a recording is now available: Thanks a…
About 5 days, 22 hours ago by: Kota Miura (@cmci_)

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RT @SuperResoluSian: We've collated all the links from our @NEUBIAS_COST webinar on SMLM analysis into a post!⬇️ From here you can navigate…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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@jennyostrop crappy-code does not mean crappy science, and it is wrong not to have that "methods" included in that science.
About 1 week, 4 days ago by: Kota Miura (@cmci_)

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@florianjug @PS_cryoEM @jug_lab @FijiSc @mpicbg @csbdresden @humantechnopole @NEUBIAS_COST @f_levet I asked the sch…
About 1 week, 4 days ago by: Kota Miura (@cmci_)

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RT @florianjug: Today at 15:30 CEST we are proud to present a bunch of useful tools! #CSBDeep #CARE #N2V #StructN2V #DenoiSeg @jug_lab @Fij
About 1 week, 4 days ago by: Kota Miura (@cmci_)

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guys, here is the major upgrade of ! #neubias thanks to…
About 1 week, 5 days ago by: Kota Miura (@cmci_)
Algorithm 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

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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).

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