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.

dijkstra3d

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

microviewer

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

kimimaro

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

sofima

Scalable Optical Flow-based Image Montaging and Alignment

zmesh

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

tinybrain

Image pyramid generation for grayscale and segmentation image resize.

pmmc

Mesh-based Monte Carlo (MMC)

biapy

Open source Python library for building bioimage analysis pipelines

pathml

Tools for computational pathology

augmenteddataloader

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

napari-mm3

Mother machine image analysis through napari

elektronn3

Utilities for 3D CNNs in PyTorch

pyssam

A Python library for statistical modelling of biomedical shape and appearance

wsipre

Handling whole-slide images with region-level annotations.