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ShahiraAbousamra / quip_mcspatnet_prediction

WSI cell detection and classification with MCSpatNet (ICCV 2021)
BSD 3-Clause "New" or "Revised" License
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Coordinates of polygons and class centers #1

Open swaradgat19 opened 12 months ago

swaradgat19 commented 12 months ago

@ShahiraAbousamra

I ran the code on a whole slide image and got the results successfully. I wanted to ask about the data that is generated.

The polygon coordinates seem to be with respect to the whole slide image, since the patch with the maximum value for patch_minx (44119) is within the image_width (46000).

My question is regarding the class centroids. There are 3 different csvs generated for the 3 classes. What is the reference frame for these class centroids? The values are ranging from 0 - 900 (approx.). Are these coordinates with respect to the patches? I'm not quite sure I understand the centroid data.

Could you please elaborate as to what reference frame you have considered for the centroids? I want to generate GeoJSON data based on the data that the code generates, so I would want to keep the frame of reference the same for the polygons and the class centroids.

ShahiraAbousamra commented 11 months ago

Hi Swarad, Thanks for using the code! The coordinates in the csv are local with the respect to the scaled down patch. The patch coordinates within the WSI are encoded in the file name. The patch file name encodes the coordinates as follows: ___. I hope this helps.