Generate grids

[Tato14]

Hi!
First, thanks for the great tool!
I was wondering how do you generate the grid tuple in the dictionary for a given image. I am struggling with coordinates and I guess I misunderstood how read_region works.
Any hints on this?

[gabricampanella]

Hello. Generating the grid tuple is entirely up to you and it depends on what data you are using. In our lb we deal with WSI and generally they come with a lot of background regions. While I could use all the tiles even if they have no tissue, it is much more efficient to only use the ones that do contain tissue. To do that we use a thumbnail of the whole slide and use simple image processing techniques no figure what tiles have tissue. About the read_region function, that comes from openslide. You just need to give it a tuple of coordinates from the ones you calculate before. I hope this was helpful.

[PlanetsR]

Hello, I am working with rat brain sections, scanned with VS120, I have a *.vsi file. On the zoomed out view I have two brain sections.
Question for setting up grid 12232019.pdf thanks Shyam.

[gabricampanella]

@PlanetsR it seems that your situation may be different. In the code I use openslide to open WSIs and extract small tiles. If you do not use openslide in your application then you would need to custom design a torch dataset class to load images.

[Naomi-Ding]

@PlanetsR it seems that your situation may be different. In the code I use openslide to open WSIs and extract small tiles. If you do not use openslide in your application then you would need to custom design a torch dataset class to load images.

@gabricampanella Hi, I'm also going to deal with WSI with a lot of background regions. Could you share your code for extracting small tiles from the WSI? Like shown in the extended data figure 7 in the paper. Thanks!

[a-dev-walker]

@PlanetsR it seems that your situation may be different. In the code I use openslide to open WSIs and extract small tiles. If you do not use openslide in your application then you would need to custom design a torch dataset class to load images.

@gabricampanella Hi, I'm also going to deal with WSI with a lot of background regions. Could you share your code for extracting small tiles from the WSI? Like shown in the extended data figure 7 in the paper. Thanks!

@gabricampanella I'd like to third this request. I'm also attempting to create a method to exclude background regions, and it would be helpful to see how you all extracted your tiles. Thank you for this fantastic project and your continued responses.