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Create post_processing.py

Open JHancox opened this issue 3 years ago • 2 comments

Description

This python script takes as input the outputs from the HoverNet network, with softmax applied to the nucleus_prediction and argmax applied to the type_prediction. It outputs an instance map along with a set of contours for each instance, which can be used to render an image overlay. This script serves as a staring point for issue https://github.com/Project-MONAI/MONAI/issues/4180

Status

Work in progress

Checks

  • [ ] Notebook runs automatically ./runner [-p <regex_pattern>]

JHancox avatar Aug 31 '22 17:08 JHancox

@KumoLiu, this is a fully functional script that Jonny has prepared for the post processing. Some of the components there, we already have implemented in MONIA but the rest of components need to be added to MONAI. It would be great if you can read this script, replace the components that are already existing in MONIA and start integrating the missing components. Please let me know if you have any question. Thanks

bhashemian avatar Sep 06 '22 13:09 bhashemian

Hi @drbeh, I'll get started to be familiar with the code as soon as possible, and will ask you for guidance if I have any questions.

KumoLiu avatar Sep 06 '22 13:09 KumoLiu

closing as as part of https://github.com/Project-MONAI/MONAI/issues/5100

wyli avatar Dec 16 '22 12:12 wyli