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EMBL BioImage Data Analysis



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Timeline of @cmci_

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RT @xuepan3: @palankarr @manorlaboratory Hi Raghva, We compared the results generated by IMARIS and Trackmate in ImageJ. There are some min…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @albertcardona: Plotting from your @FijiSc #python scripts, using ImageJ's internal plotting library, and with @jfreechart for prettier…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @CefapConfocal: If you struggle with image analysis, check our webpage with few ImageJ and Zen tutorials: ps .:…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @iefforts: The cells were visualized on a Nikon AR1 or Leica SP8 confocal microscope. At least 30 cells were analysed for each condition…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @MarJungle: BigStitcher on ImageJ for 3D model reconstructions. A beta-version is available via the Fiji Updater. I am going to try this…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ARVOtvst: New in the August issue: 25-MHz ultrasound biomicroscopy combined with #ImageJ software can be used to evaluate the opacity d…
About 3 days, 10 hours 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

CMCI weblog

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.

References for Image Analysis

Pearson, H., The good, the bad and the ugly. Nature, 2007. 447: p. 138-140. doi:10.1038/447138a; Published online 9 May 2007

Brown, C.M., Fluorescence microscopy - avoiding the pitfalls. Journal of Cell Science, 2007. 120(10): p. 1703-1705.

North, A.J., Seeing is believing? A beginners' guide to practical pitfalls in image acquisition. Journal of Cell Biology, 2006. 172(1): p. 9-18.

Pearson, H., Image manipulation: CSI: cell biology. Nature, 2005. 434(7036): p. 952-953.

Rossner, M. and K.M. Yamada, What's in a picture? The temptation of image manipulation. Journal of Cell Biology, 2004. 166(1): p. 11-15.

Cromey, D.W., Digital Image Ethics

Sampling Frequencey

Waters, Accuracy and precision in quantitative fluorescence microscopy. Journal of Cell Biology, 2009. 185(7): p. 1135-48. doi: 10.1083/jcb.200903097

Dokuwiki Configuration: URL cleaning

In local.php (not accessible so configured through configuration manager)

   $conf['userewrite'] = '1';
   $conf['useslash'] = 1;

Copied .htaccess.dist to .htaccess, then in .htaccess, *une-**commented out lines shown in Red

14 ## Uncomment these rules if you want to have nice URLs using
15 ## $conf['userewrite'] = 1 - not needed for rewrite mode 2
16 RewriteEngine on
17 #
18 ## Not all installations will require the following line. If you do,
19 ## change “/dokuwiki” to the path to your dokuwiki directory relative
20 ## to your document root.
21 RewriteBase /
22 #
23 ## If you enable DokuWikis XML-RPC interface, you should consider to
24 ## restrict access to it over HTTPS only! Uncomment the following two
25 ## rules if your server setup allows HTTPS.
26 #RewriteCond %{HTTPS} !=on
27 #RewriteRule ^lib/exe/xmlrpc.php$ https://%{SERVER_NAME}%{REQUEST_URI} [L,R=301]
28 #
29 RewriteRule ^_media/(.*) lib/exe/fetch.php?media=$1 [QSA,L]
30 RewriteRule ^_detail/(.*) lib/exe/detail.php?media=$1 [QSA,L]
31 RewriteRule ^_export/([^/]+)/(.*) doku.php?do=export_$1&id=$2 [QSA,L]
32 RewriteRule ^$ doku.php [L]
33 RewriteCond %{REQUEST_FILENAME} !-f
34 RewriteCond %{REQUEST_FILENAME} !-d
35 RewriteRule (.*) doku.php?id=$1 [QSA,L]
36 RewriteRule ^index.php$ doku.php

and also changed line 21, specified the base directory ('/').

FIJI/ImageJ Hackathon / March 15th-26th, 2010 @EMBL

for details, go to FIJI 2010 Page

Dear All,

We would like to draw your attention on the following initiative:

Fiji/ImageJ Hackathon
March 15th-26th, 2010
Room 6.51a

A group of around 15 core developers of FIJI/ImageJ will meet here at the EMBL with the aim of enhancing 3D visualization and timelapse analysis in ImageJ/Fiji.

What is Fiji?

Fiji (“Fiji is just ImageJ”) ( It emerged as a user-driven response to organize ImageJ's collection of plugins, along with comprehensive user documentation, and version-controlled code for developers. The developers introduced new ImageJ libraries for image registration, stitching, segmentation, feature extraction, 3D visualization, and numerous others.

What is an Hackathon?

It is a software development sprints. Hosting such an initiative here at the EMBL is a great opportunity for both EMBL imaging processing specialists and researchers to contribute to the open Fiji project, and have a saying in the development of this widely popular software.

Summary of the initiative


Please note that the Hachathon is an open platform however, if you want to participate please send and email to Kota Miura ( ).


17/3 (Wed) 11am @Small Operon
Erwin Frise
“Exploring spatial gene expression during early development of Drosophila”

19/3 (Fri) 11am @Small Operon
Pavel Tomancak
“New tricks for comparative genomics analysis of gene expression regulation in Drosophila”

24/3 (Wed) 4pm @Small Operon
Mark Longair
“Neuron Tracing and Computational Neuroanatomy with Free Software”

Hands-on tutorials:

17/3 (Wed, 2:30pm-5:00pm in Room 202): Image segmentation workshop
18/3 (Thu, 2:30pm-5:00pm in Room 202): Image registration workshop

If you would like to participate in these tutorials, send an email to Elisabeth Hillier ( )

For more updates on info, check

We are looking forward to hearing from you.

Best wishes,
Kota Miura (CMCI) and Francesca Peri (DB)

Advanced Microscopy Workshop

EMBL Practical Course “Advanced Microscopy” will be held next week (March 8 - 12, 2010) in EMBL Heidelberg.

Kota will give a talk on Thursday about object tracking in cell and developmental biology, and also teach practicals during afternoon of the same day.

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Weblog Archive

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