# Bioimage Analysis Wiki

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 clij moved to a new house https://t.co/XJ0YBhE2jE About 2 hours, 37 mins ago by: Kota Miura (@cmci_) RT @regagino: My postdoc work with Sarah Woolner's lab @FBMH_UoM is out @CellReports! Decoupling the Roles of Cell Shape and Mechanical St… About 17 hours, 58 mins ago by: Kota Miura (@cmci_) RT @sbarolo: #WomeninSTEM get a lot of “Reply Guys” who repeat the same unhelpful comments. @shrewshrew and I (a woman & a man in science)… About 17 hours, 59 mins ago by: Kota Miura (@cmci_) RT @cohenlaboratory: Female with microscope? Add yourself to the list! https://t.co/gN3ThsklUj About 1 day, 17 hours ago by: Kota Miura (@cmci_) RT @Dr_Fluo: The mesmerizing real-time shuttling of protoplasm within the plasmodial syncitium of the #Physarum #SlimeMold. Scarily dynamic… About 1 day, 20 hours ago by: Kota Miura (@cmci_) I did the same on Sunday hearing the news. Many of the monologues of the people were a bit remote to me when I was… https://t.co/5dZWBQPMv5 About 1 day, 20 hours ago by: Kota Miura (@cmci_)
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# 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 cmci.embl.de, click the link below to test if it is possible.

note:20110526

## 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 http://swehsc.pharmacy.arizona.edu/micro/digital-image-ethics

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 ('/').