Biomedical Image Processing Python Packages

connected-components-3d

Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)

fastremap

Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.

edt

Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.

cloud-volume

Read and write Neuroglancer datasets programmatically.

kimimaro

Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)

microviewer

Multiplatform 3D numpy image browser based viewer with voxel painting.

dijkstra3d

Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes

zmesh

Marching Cubes & Mesh Simplification on multi-label 3D images.

pmmc

Mesh-based Monte Carlo (MMC)

sofima

Scalable Optical Flow-based Image Montaging and Alignment

tinybrain

Image pyramid generation for grayscale and segmentation image resize.

biapy

Open source Python library for building bioimage analysis pipelines

pathml

Tools for computational pathology

brook-cu12

TEASAR skeletonization of 3D label volumes on NVIDIA GPUs

napari-mm3

Mother machine image analysis through napari

augmenteddataloader

Medical image augmentation tool that can be integrated with Pytorch & MONAI.

pyssam

A Python library for biomedical statistical shape and appearance modelling.

elektronn3

A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data

wsipre

Handling whole-slide images with region-level annotations.