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Biomedical Image Processing Python Packages

Python packages with the GitHub topic biomedical-image-processing. Sorted by relevance, with stars and monthly downloads.
seung-lab
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)

247K 452 49
seung-lab
fastremap

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

163K 65 9
seung-lab
edt

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

62K 264 42
seung-lab
cloud-volume

Read and write Neuroglancer datasets programmatically.

39K 173 53
seung-lab
zmesh

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

28K 72 9
seung-lab
dijkstra3d

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

23K 86 14
seung-lab
microviewer

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

22K 16 1
seung-lab
kimimaro

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

17K 202 29
seung-lab
tinybrain

Image pyramid generation for grayscale and segmentation image resize.

9K 11 0
fangq
pmmc

Mesh-based Monte Carlo (MMC)

5K 55 35
BiaPyX
biapy

Open source Python library for building bioimage analysis pipelines

2K 198 41
Dana-Farber-AIOS
pathml

Tools for computational pathology

748 452 89
google-research
sofima

Scalable Optical Flow-based Image Montaging and Alignment

630 95 20
ciroraggio
augmenteddataloader

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

395 4 0
ELEKTRONN
elektronn3

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

390 171 29
junlabucsd
napari-mm3

a plugin for mother machine image analysis

318 10 4
jvwilliams23
pyssam

A Python library for statistical modelling of biomedical shape and appearance

223 38 2
luisvalesilva
wsipre

Handling whole-slide images with region-level annotations.

145 10 5
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