# Bioimage Analysis Wiki

### Sidebar

EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

Popularity Ranking

 clij moved to a new house https://t.co/XJ0YBhE2jE About 2 hours, 56 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 18 hours, 17 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 18 hours, 18 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, 21 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, 21 hours ago by: Kota Miura (@cmci_)
blogtng:blogtop
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

# BIAS 2013 wiki page

There will be “EMBL Master course on BioImage Data Analysis” in May, and I am preparing for this course with Christoph Moehl (Bonn) and Sebastien Tosi (Barcelona). For the course we want to be interactive so we now have a wiki for the course:

We abbreviate the course title “BIAS 2013”. Registration deadline is in February, and we will be waiting for many applications!

# ImgLib2, first test

I pretty much enjoyed ImageJ User and Developer conference 2012 in Luxemburg. Interesting people from different areas in science, very exciting to see how people are doing image processing and analysis. Some of live notes could be found in my time line. One of the great contribution for the third day was Bene Schmidt's work intseg_3D, combining user clicking and active contour fitting in 3D.

One of the core topic there was ImgLib2, the generic image typ behind ImageJ2. After coming back home, I tested ImgLib2 with the Jython code below.

Results were: Started testImgLib2.py at Sun Oct 28 16:41:57 CET 2012

• ImgLib2 cursor 333 millisec
• ImgLib2 for : 138 millisec
• ImagePlus 152 millisec
• ImageProcessor 114 millisec
• Pixel Array 59 millisec

for loop using Img iterator is a bit faster than going through ImagePlus using classic nested for-loop. Even with the classic nested for-loop, using ImageProcessor was a bit faster than Img. The fastest is of course accessing pixels via pixel array. I only did this via ImagePlus, but there should be also some methods to extract an array from Img, which I did not test.

Thanks to Albert Cardona for commenting on this.

# first trial with ImageLib2
# iterations

imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif")

# accessing via ImagePlus
t3 = System.currentTimeMillis()
for i in range(imp.getHeight()):
for j in range(imp.getWidth()):
#		print imp.getPixel(j, i)[0]
imp.getPixel(j, i)[0]

t4 = System.currentTimeMillis()

# accessing via ImageProcessor
t5 = System.currentTimeMillis()
ip = imp.getProcessor()
for i in range(imp.getHeight()):
for j in range(imp.getWidth()):
#		print ip.getPixelValue(j, i)
ip.getPixelValue(j, i)

t6 = System.currentTimeMillis()

# ImgLib2 cursor
t1 = System.currentTimeMillis()
cursor = img.cursor()
cursor.fwd()
while cursor.hasNext():
cursor.next()
#	print cursor.get()
cursor.get()

t2 = System.currentTimeMillis()

t7 = System.currentTimeMillis()
for t in img:
#	print t.get()
t.get()

t8 = System.currentTimeMillis()

# pixel array
t9 = System.currentTimeMillis()
pix = imp.getProcessor().getPixels()
for i in pix:
i = i
#	print i

t10 = System.currentTimeMillis()

print 'ImgLib2 cursor',(t2-t1), 'millisec'
print 'ImgLib2 for : ',(t8-t7), 'millisec'
print 'ImagePlus',(t4-t3), 'millisec'
print 'ImageProcessor',(t6-t5), 'millisec'
print 'Pixel Array',(t10-t9), 'millisec'



# New Server

This site has migrated to a new server and also now running with the most recent Dokuwiki! You might not recognize this move and upgrade, but this could not have been done with helps and hackings by Agustin Villalba @ IT service. This Dokiwiki web application is running with sqlite3 (Dokuwiki does not deal with sqlite3 normally). Thanks to Agustin!

# Latex to Dokuwiki

I have been searching for a convinient way to convert Latex to Dokuwiki (also MSword doc to dowuwiki as well).

Never been really successful, though there are some Dokuwiki pluings that converts Dokuwiki to Latex and vice versa. Problem of the plugin is that latex should be installed in the webserver, but that is not the case in the EMBL. and I cannot install them as I am not the administrator.

## One way I figured out by now is the following detour.

1. Convert Latex document to Markdown using Pandoc.
2. Use markdown plugin (of Dokuwiki). Just copy and paste the markedown text in the dowkuwiki, and bound that part with <markdown> tag

Discovering the markdown plugin was a big change for this purpose. Not only latex docs, but MS doc and docx could be converted using the Pandoc and be pasted into Dokuwiki.

... so I wrote this short report using the markdown syntax. The plugin actually uses markdown extra, an enhanced version.

# ISBI 2012, Satellite Meeting

A picture with the ImageJ founder, Wayne Rusband.

A meeting titled “Bioimage analysis software: is there a future beyond ImageJ?” took place in Barcelona between April 31st and May 1st (http://bigwww.epfl.ch/eurobioimaging/). Some key presentations were given by Wayne Rusband, Johannes Schindlin, Curtis Rueden and all the famous developers among ImageJ community and more software such as Icy and BioimageXD.

Wayne talked about how he started developing NIH Image in 1987, with some pictures of initial Apple II machine he was developing with. The software was coded in pascal, and I told him that I started using it in 1993 and was fascinated by the ImageJ macro language. He also informed us with his latest update, pixel inspector that shows the distribution of values in the vicinity of the cursor location.

Intensive discussions on strengthening the community was held as well, mainly in the direction of setting up a core portal and planning periodic meetings.