Posted by
No Name-4 on
Apr 19, 2011; 3:14pm
URL: http://imagej.273.s1.nabble.com/Whole-slide-image-analysis-with-ImageJ-tp3684908p3684910.html
Hi Johannes,
I agree that it would be great to see this code in the public domain. We will contact Dr. Zerbe and see if he is able to provide his code back to the IJ community.
In our lab we deal exclusively with these 'whole slide' images - we currently have ~60,000 slides scanned. I have been using ImageJ (and NIHImage) for analysis of 'field-of-view' images for the last 15+ years so I am very interested to see development in this area. As I see it, there are perhaps two different tasks when working with this image type: 1) analyzing tiles from the whole slide file with generation of markup tiles (or ideally a reconstructed whole slide markup file) and 2) viewing the multiscale whole slide images and markups. Ideally, both of these functions will find their way into the new versions of ImageJ that the team is hard at work on.
I have tried using the LOCI Bioformats Importer plugin to do task #1 but I think that I am running into memory issues even with the 'Virtual Stacks' option checked. We have been using the vendor's (Aperio) 'Extract Region' tool to generate 5000x5000 pixel jpg tiles to folders and then batch processing the files with ImageJ. One challenge is reviewing the markup tiles after analysis and putting the individual tiles in the context of the whole slide image. Another problem is that the extraction process is extremely slow and we don't have an obvious way to batch extract multiple whole slide files. I would like to hear from the user community if anyone has developed a successful strategy for dealing with these images.
It sounds like Aivar Grislis did some work on dealing with large sized images (at least for viewing) at the Hackathon: "Initial development toward a multi-resolution tiled viewer for IJ2 (Aivar Grislis)" I would be interested in hearing from Aivar about his experience working on this project. From the roadmap, it sound like this particular feature is slated for rel 2.5.
Cheers,
Jim
-----Original Message-----
From: Johannes Schindelin [mailto:
[hidden email]]
Sent: Monday, April 18, 2011 4:57 PM
To: Deeds, James
Cc:
[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