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vqdang / hover_net

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.
MIT License
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Running hovernet only on masks #260

Open ajinkya-kulkarni opened 1 year ago

ajinkya-kulkarni commented 1 year ago

Hello team, thanks for this repo! I was wondering if hovernet can be run to infer only on masks? Specifically, sometimes I find that StarDist does a better job at segmenting the nuclei from H&E Images, but I would be interested then to run hovernet on the StarDist segmented masks to generate the classes information. Any idea if I can do that and if yes, how?

Thanks, Ajinkya

simongraham commented 5 months ago

I wouldn't recommend running hovernet only on masks, as you will still need the RGB input to make a good prediction.

However, if you wanted you could use the instance segmentation from StarDist and the TP branch output from HoVer-Net. Then, you could provide a majority vote of the TP output within each instance.

So, you would need to run both models separately and then combine the output.