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H&E .scn files+Developer

Forum » Definiens Community Forum » Rule Set Development Talk
User: amalysa
Since: 02/13/2012
Rule Sets: 0
User Posts: 2
Date: 02/14/2012 [04:52 PM]
Hi,

I need help figuring out how to process 40x H&E stained .scn files using Developer to batch process a large number of slides. What I would like to do (for now) is the following with these images:

i) detect the nuclei and determine their shape and sizes
ii) determine nucleus to cytoplasm ratios

However, I'm having a really hard time gettin past the segmenting stage as well as classifying the different parts of the tissue. For instance, when I open the high quality .scn files in Developer 2.0 and try to segnment it, the process takes hours. I was recently told that I should make a map of the low quality image and then the high quality image in after.

When I've segmented the tissue, classifying the different cells has become almost impossible because I don't know what features to use to be able to detect differences to classify different objects.

I know I've just asked for a lot of help but I really am lost as to how to get past these points in my analyses. Does anyone have any experience with working i) on high quality .scn files, and ii) analyzing H&E stains using Developer. My background is basic in working with Definiens and writing rulesets.

Thanks for taking the time read my message and for all your help icon_smile.gif
Profile
User: thaberichter
Since: 12/06/2007
Rule Sets: 1
User Posts: 5
Date: 02/24/2012 [10:24 AM]
Dear Amalysa,

the short answer to your question is;
1. you need to do tiling-and-stitching (subset-based or map-based)in order to be able to work on image fragments of reasonable size. I would try full resolution or down to 10x
2. There are several strategies for segmenting nuclei in H&E, one of them being the so-called multiresolution-segmentation-optimization, which is taught in our Advanced II 2D Academy course.

I am not sure how much training you have had so far, but if you don't miond we can have a conversation offline on how to best provide you with the skills and support that you need.

Best wishes,
Thomas Haberichter
Director Technical Field Operations North America

[This article was edited 1 times, at last 24.02.2012 at 10:25.]
Profile
User: amalysa
Since: 02/13/2012
Rule Sets: 0
User Posts: 2
Date: 03/09/2012 [03:53 PM]
Hi Thomas,

Thanks for your message, but I've trying to get in contact with you since your post. Whenever you have some extra time, would you kindly respond back to me?

Thanks so much
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