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:

http://cmci.embl.de/shared/bias2013

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

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.

Addendum: See also proper benchmark in the following link in ImageJ2 site:

http://developer.imagej.net/imglib-benchmarks

Thanks to Albert Cardona for commenting on this.

<sxh python> # first trial with ImageLib2 # iterations

from net.imglib2.img import ImagePlusAdapter

imp = IJ.openImage(“http://imagej.nih.gov/ij/images/blobs.gif”) img = ImagePlusAdapter.wrapReal(imp)

# 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'

</sxh>

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!

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.

Coupled lectures on Classification and Clustering will be given in the CMCI seminar in April and May. These two approaches have been widely used for screening and system descriptions, but there seems to be more in the future in terms of image processing and analysis, as we have seen in the CMCI seminar in March. For this reason we asked for introduction for these two topics by two experts in the EMBL. Bernd Fischer will give us a lecture on Classification and Machine learning, and Jean-Karim Heriche will give a lecture on cluster analysis.