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EMBL BioImage Data Analysis

EuBIAS

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Timeline of @cmci_

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an open position for a bioimage analyst, Antwerp https://t.co/KInzDwy4bd
About 12 hours, 42 mins ago by: Kota Miura (@cmci_)

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RT @napari_imaging: Thanks to all our contributors! If you're interested in learning more about how to use napari then join our upcoming w…
About 5 days, 15 hours ago by: Kota Miura (@cmci_)

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RT @oozguc: Due to the circumstances, we are postponing the meeting to June 12; hopefully, a time we can all go back to scientific and inte…
About 6 days, 12 hours ago by: Kota Miura (@cmci_)

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RT @jytinevez: We finished listing and formatting the Q&A we had during the #TrackMate session of the @NEUBIAS_COST #NEUBIAS_Academy even…
About 6 days, 19 hours ago by: Kota Miura (@cmci_)

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RT @EntraCod: @olivier_debora @jytinevez @NEUBIAS_COST Or in other words, we are doing this for a very specific case rather than generic on…
About 6 days, 19 hours ago by: Kota Miura (@cmci_)

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RT @BoSoxBioBeth: Available now on Youtube at the link below. Thanks @NEUBIAS_COST for having me, it was a ton of fun to talk about @CellP
About 6 days, 19 hours ago by: Kota Miura (@cmci_)
blogtng:blogtop
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




CMCI weblog

DeadEasy Caspase ImageJ plugin

There are often cases I see that ImageJ plugins that seems to be very useful is not linked to ImageJ plugin site. Here is one case, I just happened to find.

DeadEasy Caspase ImageJ plugin

“Here, we present a method based on image filtering and mathematical morphology techniques, to count automatically the number of dying cells in intact fruit-fly embryos. We call the resulting programme DeadEasy Caspase. It has been validated for Drosophila and we present examples of its power to address biological questions. Quantification is automatic, accurate, objective, and very fast.”

http://www.biosciences-labs.bham.ac.uk/hidalgo/software.htm

description is http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005441

Lecture Notes: FRAP internal course

Lecture Notes: FRAP internal course is now available (not completed yet but…). More will be added by Sebastian Huet and Christian Tischer later on.

jsMath plugin installed

Installed jsMath plugin, for using tex code directly in this wiki. Some problems seems to appear with previous text with .htaccess codes, but will fix later.

further notes: 2010 Apr. 21
I initially used jsMath to show math equations but then realized that mathJax is more up-to-date module for doing this (mathJax actually is de facto jsMath2.0). I then switched to mathJax.

MathJax works well with Chrome when you view this page. But then soon I found out that this is possible with only Chrome, not with Firefox nor IE. Since most of people visiting this site use Firefox, I started to try configuring but did not work with many different trials… then finally I found a solution for Firefox; upgrade it. The problem I had in viewing math equation was occurring with version 3.0x (on win32), and this does not happen and works well when version 3.6.3 is used. It was as simple as that. without thoughts, I was thinking that “My Firefox should be pretty new”.

The problem I encountered seems to be due to difference in the web-font loading settings. With IE, one better try to use at least IE9. I have not tired this yet, and probably will not because I have not seen any visitor using IE these days.

By the way, if you want to test if your browser is enabled with viewing math equation in cmci.embl.de, click the link below to test if it is possible.

http://cmci.embl.de/mathjax/test/

note:20110526

a disadvantage after installing jsMath plugin is that the page loading became significantly slower than before.

Blocking spam

There has been Spam comments rushing in so I set the comments to be only available through CAPTCHA.

FRAP manual updated

There is always some confusion when deriving Diffusion coefficient after Soumpasis fitting in FRAP, whether to use radius or diameter for the parameter “w”. As manual has been saying, this “w” is indeed radius, not diameter. I made a bit of stress on this part.

http://cmci.embl.de/documents/frapmanu

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Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)