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kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
100 stars 31 forks source link

Watershed uses only one CPU and runs very slow on large volumes #270

Open qin-yu opened 6 months ago

qin-yu commented 6 months ago

I'm running PlantSeg for FOR2581 but found watershed step uses only one CPU. I'll try to improve it but please stop me if it's not possible @lorenzocerrone

lorenzocerrone commented 6 months ago

Parallelizing the distance transform might be possible in Vigra, but I think the watershed is single-core only

qin-yu commented 6 months ago

Parallelizing the distance transform might be possible in Vigra, but I think the watershed is single-core only

Cry :' (

It took > 35 minutes to run watershed on a clear nuclear boundary pmap of size [473, 1712, 1712]! I have 63 cores idling 

INFO:  PlantSeg Napari info - 15:15:55 04.06.2024 - Watershed Segmentation: Widget Watershed Segmentation computation started
Missing chrome or resource URL: resource://gre/modules/UpdateListener.jsm
Missing chrome or resource URL: resource://gre/modules/UpdateListener.sys.mjs
INFO:  PlantSeg Napari info - 15:51:27 04.06.2024 - Watershed Segmentation: Widget Watershed Segmentation computation complete in 2132.12s