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EMBL BioImage Data Analysis



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RT @LauLauThom: Just updated the Roi 1-click tools with a cool feature 🥳 Keep the left-click maintained to preview the roi and adjust its p…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

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@KuglerElisabeth @martinjones78 @dgaboriau @WilsonAdams_ @focalplane_jcs @AcademicChatter @NEUBIAS_COST
About 2 days, 8 hours ago by: Kota Miura (@cmci_)

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RT @KuglerElisabeth: How can #developers help wet lab #scientists to use their analysis approaches? What's your thoughts? Interesting que…
About 2 days, 8 hours ago by: Kota Miura (@cmci_)

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RT @paqio: Exciting new all-optical data, fresh off a new prototype! Showing off beautiful holographic optogenetic activation of the cir…
About 3 days, 17 hours ago by: Kota Miura (@cmci_)

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thank you, thank you, and thank you!
About 5 days, 12 hours ago by: Kota Miura (@cmci_)

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About 6 days, 9 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

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, click the link below to test if it is possible.


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.

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 ('/').

entry generator

Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 12:46 (external edit)