Posted by
Toby Cornish on
Jan 09, 2008; 6:13am
URL: http://imagej.273.s1.nabble.com/ImageJ-driving-AVT-Guppy-CCD-cam-tp3697467p3697472.html
Melissa,
It would be great if we could get some an imageJ plugin for the Aperio file format. I would like to warn you somewhat about what you are getting into, though. As far as I understand it, the .svs file is a container format that can contain tiff, LZH compressed tiff, jpeg or jpeg2000 images. These are generally whole slide images and typically run around 120 MB per file for a 20x, highly compressed jpeg2000 image. That is somewhere around 1.5 gigapixels for a typical 20x slide. At 40x, the situation is even worse.
So, there are really two issues with opening these files in imageJ. First,jpeg2000 (which b/c of image size, is the defacto default encoding for whole slide images) isn's supported by imageJ, although java libraries exist for handling the encoding. More concerning, is the massive size of these images. This will probably necessitate a lot of display tricks such as paging portions of the image into memory and using prescaled lower resolution images (included in the svs file) for zooming. I am not sure how much of this imageJ would support without a lot of new code or some serious hacks. Of course, I could be wrong and maybe large image support was added to imageJ at some point.
So, I think adding .svs file support in considerably more than coding up import/export filters. That stated, there are MANY people that would love to see new tools for working with these files. The lock-in with Aperio is frustrating, especially when all of your analysis methods are imageJ-centric. If you are serious about getting some form of support for .svs files in imageJ as a plugin or otherwise, I would be glad to do whatever I could to aid you.
toby
> Date: Mon, 7 Jan 2008 14:01:44 -0500
> From: Yan Gao <
[hidden email]>
> Subject: Re: I would like doing image analysis of svs file by using imageJ
>
> Hi, Melissa.
>
> Thank you very much for your offer. Yes, I can send you some files. The
> files are too big, you need let me know how I can put the files in your
> server. I really appreciated your help.
>
> Best Regards,
>
> Yan
>=====================================
>
>Yan Gao, Doctoral of Science, HTL (ASCP)
>Novartis Institutes for BioMedical Research
Toby C. Cornish, M.D., Ph.D.
Pathology Resident
Johns Hopkins Medical Institutions
[hidden email]