About proc_kumar_ann.py

Hi. Thank you for the awesome code. I have a problem to understand this code on the 63rd line of proc_kumar_ann.py :

for idx, inst_map in enumerate(insts_list):
    ann[inst_map > 0] = idx + 1

Why the values of annotation are given the idx of insts_list? Doesn’t this lose the segmentation information?

[simongraham]

Also, if your intention for this question was to convert the xml Kumar labels to a 2D array, then you can also use the labels that we have organised in the google drive link below:

https://drive.google.com/drive/folders/1l55cv3DuY-f7-JotDN7N5nbNnjbLWchK

Here, for CPM and Kumar the Labels are stored in an array size HxW where each nucleus is given a unique value. i.e the nuclei are labelled from 1 to N, where N is the number of nuclei in the image and 0 is the background. For CoNSeP, the Labels are stored in an array size HxWx2. The first channel is the same as described above and the second channel indicates the type of nucleus. For a more in depth description of this, look at the README file when downloading the CoNSeP dataset from this page.

[simongraham]

We are now closing this issue. Thanks for using our code and let us know if you have any further questions 👍