Replicate workflow for nuclei segmentation and shape measurements - Githubissues

beatrizserrano / BH2024-project17

Repository to manage project 17 at the BioHackathon Europe 2024

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Replicate workflow for nuclei segmentation and shape measurements #21

Open sunyi000 opened 3 weeks ago

sunyi000 commented 3 weeks ago

replicate this simple workflow in Galaxy
draft workflow is created here
registered in dev workflowhub https://dev.workflowhub.eu/workflows/1364

TO DO:

before 'threshold' step, add some preprocessing steps, e.g. smoothing
make it work with 3D image
try replacing 'threshold' and 'label map' with cellpose
post processing after measurements, for example, once we have the tables, find out eccentricity, no. of circles etc.