Recommend users a halo for U-Nets - Githubissues

kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

https://kreshuklab.github.io/plant-seg/

MIT License

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Recommend users a halo for U-Nets #252

Closed qin-yu closed 1 month ago

qin-yu commented 1 month ago

This PR provides users a theoretical minimum halo for U-Nets, but in practice a smaller halo may also work well.

Changes

This PR attempts to fix #251

[x] Compute a halo based on model architecture
[x] Recommend users a halo for selected PlantSeg-compatible models (can be toggled off)
[ ] Recommend users a halo based on images and architecture

Definition

Reference: Exact Tile-Based Segmentation Inference for Images Larger than GPU Memory