Tissue masking about pathology-whole-slide-data HOT 7 CLOSED

Hi Michel,

Yes, indeed the intersection can then be done on polygon level. And yes you can use that function to convert a NumPy array to polygons. You can use a spacing value of ~4.0 or ~8.0 (.get_slide) when opening the mask (please use the asap backend, because openslide backend does not work well with monochrome images) and upscale the polygons.

For creating tissue masks I recommend using this algorithm

Best wishes,
Mart

from pathology-whole-slide-data.

Hi Mart,

Okay, all clear! Thank you very much for the explanation.

Best,

Michel

from pathology-whole-slide-data.

Hi Michel,

If it is still pending, maybe you can contact Peter Bandi he has created this algorithm.

from pathology-whole-slide-data.

from pathology-whole-slide-data.

Dear Michel,

There are two options available already.

The first one is by using the MaskAnnotationParser
This parser converts a mask into multiple rectangle regions for which the size can be specified.

Another option, which I would recommend, is to create polygons from the tissue mask with this function
With the Shapely library, you can intersect the tissue mask polygons and the annotated polygons. From the intersection you create a new annotation file, e.g., with write_asap_annotation or use the internal JSON representation of wholeslidedata convert_annotations_to_json. In this way you get a cleaned annotation file which you can use for training.

I hope this helps and please let me know if anything is unclear.

Best wishes,
Mart

from pathology-whole-slide-data.

Dear Mart,

Thanks for the suggestions. I think the second option, where a clean annotation file is created, is indeed preferred. If I understand it correctly we then find the intersection between the tissue region and the annotation region on polygon level.

This function converts a tissue mask (Numpy) to polygon format and assumes that I have already obtained a tissue mask as well, right? What would you recommend to obtain the tissue masks themselves?

Best,

Michel

from pathology-whole-slide-data.

Hi Mart,

I requested access to the algorithm that you mentioned, but its still pending. Do you perhaps know who I would have to contact to get permission?

Best,

Michel

from pathology-whole-slide-data.