bism 0.0.6

Biomedical Image Segmentation Models (BISM)

bism - Biomedical Image Segmentation Models

This is a collection of generic PyTorch model constructors usefull for biomedical segmentation tasks. Something akin to the timm package for 2D image tasks. When at all possible, each model will offer a 2D or 3D implementation, however we will not provide pre-trained model files.

Current Models

Model	2D	3D	Scriptable
UNet	✓	✓	✓
UNeXT	✓	✓	✓
Recurrent UNet	✓	✓	✓
Residual UNet
Unet++	✓	✓	✓
CPnet	✓	✓	✓

Current Generic Blocks

BLOCK NAME	2D	3D
UNeXT Block	✓	✓
ConcatConv	✓	✓
Recurrent UNet BLock	✓	✓
Residual UNet BLock	✓	✓
DropPath	✓	✓
LayerNorm	✓	✓
UpSample	✓	✓
ViT Block

Segmentation Implementation

APPROACH	2D	3D
Cellpose
Affinities		✓
Local Shape Desc.		✓