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EMBL BioImage Data Analysis



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Timeline of @cmci_

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RT @SimonFlyvbjerg: Image analysis job opening in Wonderful Copenhagen
About 11 hours ago by: Kota Miura (@cmci_)

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RT @JekelyLab: Interested in connectomics? Join us in stunning Exeter! Postdoc opening to work on Platynereis serial EM data @UoE_Jobs @Uni…
About 11 hours, 1 min ago by: Kota Miura (@cmci_)

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I like this kind of analysis - protein and organelle distributions
About 11 hours, 4 mins ago by: Kota Miura (@cmci_)

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Measuring radial intensity profile using custom IJ macro. Fig4b.
About 11 hours, 5 mins ago by: Kota Miura (@cmci_)

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RT @SfPRocur: One hashtag to follow for this kind of #sciart is #cellfie - different kinds of cells usually captured in a microscope. Look…
About 22 hours, 36 mins ago by: Kota Miura (@cmci_)

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RT @herrsaalfeld: Oh---look what just came out: @funkstille @srinituraga @cremi_challenge
About 23 hours, 55 mins ago by: Kota Miura (@cmci_)
Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin

CMCI weblog

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.

Previous Headline news

just to keep some memo on previous news:


- Peter Serocka's talk "Visual Analysis Tools for Multivariate Image Data" on Jan 29th, 2010, from 11am at the small operon
 (18. Jan. 2010).

- CMCI symposium 2nd round, a series of talks by EMBL researchers on Sept 25th, 2009
 (29. Aug. 09).

- CMCI symposium, a series of talks by EMBL researchers on June 30th, 2009
 (29. june. 09).

- FRAPcalc updated and now Ver.9g.
 (11. Dec. 08).

- “Running 3D-Projector” now downladable (29. Aug. 2008).

- “Spindle FRAP/FLIP analyzer” now downloadable (12 Aug 2008).

- CMCI seminar: July 31st (Thu) 2008, 15:00- 16:00 @small operon

 Anke Meyer-Baese (Florida State University) will talk about “Pattern Analysis and Visualization in Computer-Aided Diagnosis:Cross-Fertilization between Biomedical Imaging and Engineering” (–> Abstract)

- “Time Series Color Coder” added in download section, and FrapCalc was updated to ver.9e (24. Jul. 08)

- CMCI seminar: July 25th (Fri) 2008, 11:00- 12:00 @ large operon  by Robert Murphy (Carnegie Mellon University) –> “Automated Determination and Modeling of Subcellular Location for Systems Biology” (–> Murphy lab website)

- Next CMCI seminar: Jan 21 (Mon) 2008 11:00-12:00 @ small operon
Christian Tischer (The Institute for Atomic and Molecular Physics, Amsterdam) will talk about measurement of microtubule dynamics using his automated MT tracking system.  Title: “Spatial Regulation of Microtubule Dynamics in Fission Yeast” For more details, see his Abstract.

- CMCI seminar on oct. 26 (Fri) 14:00
speakers: Jerome Solon and Kota Miura

- FRAPcalc updated and now Ver.9a. Leica .cvs format is loadable now (27. Aug. 07).

- CMCI seminar on Aug. 22 by Shigenori Nonaka (Dept. Imaging Science, NIBB Japan) about motor protein and left-right asymmetry (details).

- added “DeltaVision Format Header Reader” in the download section (13 June  2007)
- Young-Tae Chang (Dept. Chemisty, NYU) will give a talk titled “Colorful Chemical Genetics” on June 15th. More details –> seminar page (5.June.2007)

- added “File Converter - Perkin Elmer Tiff Series to 3D stacks” in the download section (5.June.2007).
- Emre Yaksi (Dept. Biomedical Optics, MPI-Medical Research) will give a talk “Imaging odor responses in zebrafish forebrain by using two-photon microscopy” on 25th of May. (16. 04.07) check his paper –> (Link)

- Prof. Ralf Schnabel (Technical University of Braunschweig) will present a softwar SIMIBiocell, a tool for automated analysis of cell lineages (details).

- Download page initiated (updated FRAP_calc and documentation) (28.Mar.07)

- ImageJ Plugin Programming Course Slide Show in this page (1.03.07)

- ImageJ Macro Programming course Slide Show in this page (20.02.07)

- CMCI Mini-Symposium: Progress of Mathematical Morphology in Biology on Feb. 6th. Members from Centre of Mathematical Morphology @ Ecole des Mines de Paris will present their works.  Talks will be broadcasted and shown in the EBI also.

- Slide show of Image Processing / Analysis internal course is available in this page. (need Flash player plugin installed)

- New Tracking ImageJ PlugIn: Particle Tracker (27.11.06)
- New Tracking ImageJ PlugIn: MTrackJ (27.11.06)


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