3d Segmentation Python Packages

fishfeats

Napari plugin for spatial RNA quantification

segmentation-models-3d

Set of Keras models for segmentation of 3D volumes .

u-segment3d

Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

octopi

Search for Protein 3D Coordinates in CryoET Tomograms

fastai-sparse

Fastai extention for sparse 2D-3D like pointclouds and triangle meshes

pytorch3dunet

Versatile U-Net implementation for volumetric semantic segmentation written in PyTorch

pytorch3dunet-smax

3D U-Net model for volumetric semantic segmentation use in SpotMAX

pytorch3dunet-spotmax

3D U-Net model for volumetric semantic segmentation use in SpotMAX

ct-segnet

Automated 3D segmentation powered by 2D convolutional neural networks