[ImageJ-devel] Parallel image processing using ImageJ in the Cloud

[Daniel James White]

Hi Jimmy,

On Apr 6, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Mon, 4 Apr 2011 22:37:44 -0700
> From:    Jimmy Su <jimmy at OPTILLEL.COM>
> Subject: Parallel image processing using ImageJ in the Cloud
> 
> We recently completed a Phase 1 SBIR project with OSD on the topic of
> analytic tools in the Cloud.  To demonstrate our tool's ability to
> construct image processing workflow and deploy the generated code to
> the Cloud, we took ImageJ and added some Cloud processing capabilities
> by using the MapReduce framework.

Sounds very nice, and is certainly of interest to the imageJ community...
as we are moving towards systems biology approaches where
massively parallel computing is a requirement. 

Around here we have a small cluster 100 nodes or so runbning sun grid engine,
and also access to the larger cluster in Dresden's TUD. 

We don't have experience with the Amazon cloud systems ... yet...

ImageJ2 will have a better design for running in a headless (no GUI) manner, 
which should help a great deal with this kind of stuff. 
Many imageJ plugins are tied to a GUI, and cant be run headless...
in the future that will no longer be a limitation for a properly written plugin. 

see
http://imagejdev.org/

maybe you might like to get involved?

> 
> We added Cloud processing capability to ImageJ by adding a Hadoop
> InputFormat to handle image types in HDFS (Hadoop Distributed File
> System) and encapsulating ImageJ operations in map and reduce methods.
> This significantly increases ImageJ's throughput in processing
> images.  Attached is the running time chart showing processing time
> decreases from over 5 hours on two nodes to 15 minutes on 64 nodes on
> Amazon EC2.  

can you send that attachment to be personally, as thee mailing list ate it. 

> Are there any interests in the ImageJ community for
> parallel processing in the Cloud?

Yes, very great interest. 

>  What kind of applications are you
> developing that needs ImageJ processing in the Cloud?  

High content screening, many thousands to millions of images
to be processed in pipelines, or even with decisions made on the fly, 
classification of phenotypes from images.... 

Cell profiler is currently better geared to this job than imageJ, 
but they play nice together. 

> We would love
> to hear your feedback.  Thank you very much for your time.

the ImageJ-dev and Fiji teams are where this stuff is happening...
there are mailing lists and IRC channels where you can chat to 
those who know more about it than me....

and this is our invitation to communicate directly with the interested developers 
of imageJ2 and Fiji
 (
http://pacific.mpi-cbg.de		Fiji -  is just ImageJ (Batteries Included)
)

cheers

Dan

> 
> Jimmy

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities 
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net 	BioImageXD
http://pacific.mpi-cbg.de		Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk		Dan's Homepages
https://ifn.mpi-cbg.de 			Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )