3d Segmentation Python Packages

python-elf

Utility functions for large-scale bio-image analysis.

fishfeats

Napari plugin for spatial RNA quantification

octopi

Search for Protein 3D Coordinates in CryoET Tomograms

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.

segmentation-models-3d

Set of models for segmentation of 3D volumes

fastai-sparse

3D augmentation and transforms of 2D/3D sparse data, such as 3D triangle meshes or point clouds in Euclidean space. Extension of the Fast.ai library to train Sub-manifold Sparse Convolution Networks

pytorch3dunet

3D U-Net model for volumetric semantic segmentation written in pytorch

ct-segnet

CTSegNet is an end-to-end 3D segmentation package for large X-ray tomographic datasets using 2D fully convolutional neural networks (fCNN).

pytorch3dunet-spotmax

3D U-Net model for volumetric semantic segmentation written in pytorch

pytorch3dunet-smax

3D U-Net model for volumetric semantic segmentation written in pytorch