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(how) can apply my own image?

Open duernaT opened this issue 3 years ago • 3 comments

I noticed your paper (very nice work!) mention about HistoSegNet can generalize to other datasets without retraining. If I am not misunderstanding, I can load my own image and get the segment information?

If so, can you point out how to input my images?

With many thanks, Duerna

duernaT avatar May 14 '21 07:05 duernaT

Hello Duerna, yes, HistoSegNet can generalize to other datasets without retraining, assuming that:

  • They are histopathology images using stains found in our dataset (e.g. H&E) and not fluorescent scans
  • You rescale your images to fit the same microns/pixel resolution stated in our paper and then reshape to the 224x224 pixel resolution the model uses as input
  • The organs present in your histopathology images are roughly the same as those mentioned in our paper

If those requirements are met, then you can drop your images into a new sub-folder of the "img" folder and set the "input_name" parameter of HistoSegNetV1 accordingly. You can check out "demo_01_segment_patches.ipynb" for an example.

lyndonchan avatar May 14 '21 17:05 lyndonchan

Thank you so much.

I have the HE-stain pictures that reshaped to 224x224 pixels. And then drop the images to "img" and set the HistoSegNetV1. However, I have tried several times, it not work with my images.

Here are they: GTEX-VJYA-1526_0575 GTEX-VJYA-1526_0909 GTEX-VJYA-1526_1394 GTEX-VJYA-1526_1560 GTEX-VJYA-1526_1812

Can you please kindly point out how can I apply my img to the HistoSegNet?

Best regards, Duerna

duernaT avatar May 17 '21 00:05 duernaT

hi,i want to know that after I have got the segmentation result of each patch,how can I merge the patches to the origin size of the WSI

guascy666 avatar Sep 08 '23 13:09 guascy666