An extension for whole slide microscopic images

Development
1

Dear All,

Whole slide microscopy histopathology images can be as large as several GB in file size, with jpeg compression. I’m preparing an extension that uses python script module to dynamically load portions of the whole slide image (WSI) at the desired resolution into the current Slicer view.

I put some basic info at:

I’m hoping to add this through the extension management system and would like to hear about your suggestions/opinions.

Thanks!
yi

NOTE: The extension has been renamed to BigImage

2 Likes
2

This looks great, thanks @gaoyi.cn :+1:

It would be cool to try this out with some of the >14TB of microscopy data recently made available via IDC.

3

Thank you Steve!

I have added the s4ext file to the extension index and created a pull request.

However when I was trying to create another PR for the shape analysis module, seems the two PRs are considered as one?

Not sure how i can retrieve the later one and do it in a separated PR…

Thanks for advice!

Best,
yi

4

Hi Yi -

It sounds like perhaps you created the second pull request as a branch off the first pull request. That would link them together in github. To confirm the process, you should first checkout the mater branch of the extension index, create a branch for the first extension, add the file and push to github to create the first PR. Then you checkout the master branch again, create a second branch for the second s4ext file, and then push the second branch to github to create a second PR. Then each PR will have and independent history. Can you try that?

Cheers :+1:
Steve

5

Hi Steve,

Yes that’s was the situation… I’ll do again following your advice.

Thanks!

Best,
yi

6

Hi Steve,

the new PR is created and the comments and suggestions in the previous PR by Andras and James have been addressed.

Thanks!
yi

7

Dear @gaoyi.cn Dr. Gao,
The SlicerScope extension is not visible on Slicer 5.0.3.
Would you please guşde me how to install your module.
Best wishes
Serdar Balci, MD, Pathologist

8

@sbalci it appears @gaoyi.cn renamed SlicerScope to SlicerBigImage so look for “BigImage” in the extensions manager.

9

Hi,
I could not find it either. They do not appear in extensions or modules.

I tried to built from github source but I could not do it.

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10

It does not appear under extension builds either:

https://slicer.cdash.org/index.php?project=SlicerStable&filtercount=1&showfilters=1&field1=site&compare1=63&value1=BigImage

11

The BigImage extension was only submitted to the Extensions Index of Slicer-5.1, but not for Slicer-5.0. I’ve submitted it now, so if the extension is compatible with Slicer-5.0 then it will show up in the Extensions Manager in Slicer-5.0.3 tomorrow. Until then you can use Slicer-5.1.x (the latest Slicer Preview Release).

12

Dear @lassoan thank you very much. I have switched to 5.1 version and I can download the module now.

@gaoyi.cn also reached me and instructed to 5.1.

thank you both.

I hope to use it in our group’s pancreas research.

Best wishes.

Serdar