Posted by
Vitali Khvatkov-2 on
Apr 18, 2011; 10:05pm
URL: http://imagej.273.s1.nabble.com/Whole-slide-image-analysis-with-ImageJ-tp3684908p3684913.html
We have done similar implementation of ImageJ on our web-server platform and
I can share some thoughts and issues that are involved in this process (by
the way, same issues are involved in utilizing ImageJ on map/reduce
computing clouds).
- This application cannot be a plug-in to ImageJ - this has to be server
application stack that is actually using ImageJ as plugin (we do the same)
- Using non-overlapping virtual tiles does not work very well for kernel
operations (e.g. Unsharp) because it creates ugly edge effects (we have to
use larger virtual tiles and trim them although it adds processing
"overhead" )
- Example of analysis: Unfortunately, the biggest problem with high
performance image processing using ImageJ is not ImageJ core but plugins
that are largely not designed and built for High Performance Computing (they
may leak memory, create operations "overhead" etc.). So we had to implement
policing process that just kills ImageJ processes every so often but this is
expensive resource wise. ImageJ was written to make plugin development as
easy as possible, with virtually no controls. So when ImageJ 2 becomes
available, plugins have to be reviewed and adapted for high-performance
computing.
If somebody would like to see and try to use ImageJ plugins on server as
tile processors for whole slide images, let me know. We will be happy to
provide this resource for ImageJ community. We cannot let people push Java
code to our production servers but if somebody has Windows server (physical
or on Amazon Compute Cloud) and would be willing to let community members
use it, we will be happy to set it up for everybody to use.
Vitali
Smart Imaging Technologies Co.
713-589-3500
www.live.simagis.com
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
Johannes Schindelin
Sent: Monday, April 18, 2011 3:57 PM
To:
[hidden email]
Subject: Re: Whole slide image analysis with ImageJ
Hi James,
On Mon, 18 Apr 2011, Deeds, James wrote:
> I just ran across the article cited below describing a plugin for
> viewing and analyzing scanned whole microscope slides using ImageJ. I
> would be interested in trying the plugin out or hearing feedback from
> others who may have used the tool. I understand that support for whole
> slide image formats is planned for the big ImageJ 2.0 project underway.
> Perhaps Dr. Zerbe has some useful input for the ImageJdev team.
>
> Distributed computing in image analysis using open source frameworks
> and application to image sharpness assessment of histological whole
> slide images Norman Zerbe, Peter Hufnagl, Karsten Schlüns Diagnostic
> Pathology 2011, 6(Suppl 1):S16 (30 March 2011)
>
http://www.diagnosticpathology.org/content/6/S1/S16Sadly, the requirement of other scientific fields for full disclosure of
methods (including tools) has not made it quite yet into life sciences.
That is the only reason I can see why the paper describes a plugin that is
not available publicly.
Therefore I doubt that you will get much feedback from people who used it.
Unfortunately, this is also the reason why nobody involved in the ImageJDev
project can form an opinion about, or benefit from, the work described in
the paper, except by putting an undue burden on the developers who are
already working very hard on a first beta release of ImageJ 2.0.
Maybe you want to contact the corresponding author, and maybe the author
wants to contribute a bit back to the free software he benefitted from so
nicely? Maybe there is a chance to avoid reinventing the wheel here? Maybe
this is a perfect opportunity to stand on each others shoulders?
Ciao,
Johannes