Connectomics Python Packages

edt

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

68K 269 42

cloud-volume

Read and write Neuroglancer datasets programmatically.

28K 176 54

kimimaro

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

25K 219 30

grandiso

Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")

23K 66 10

fpzip

Cython bindings for fpzip, a floating point image compression algorithm.

21K 36 5

connectomics

Common repository for connectomics-related libraries.

14K 67 17

caveclient

This is the python client for accessing REST APIs within the Connectome Annotation Versioning Engine.

13K 43 19

skeletor

Extraction of 3D skeletons from meshes.

10K 261 31

zmesh

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

7K 76 9

compresso

Compresso: Efficient Compression of Segmentation Data For Connectomics

7K 4 1

sofima

Scalable Optical Flow-based Image Montaging and Alignment

4K 102 24

igneous-pipeline

Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.

3K 69 24

brainfc

Resting-state fMRI functional connectivity, connectome, brain network and hypergraph analysis in Python with a local GUI. 静息态 fMRI · 功能连接矩阵 · 脑网络 · 超图分析

2K 5 0

cits

Python package for CITS algorithm: Causal inference from time series data

2K 1 0

brook-cu12

TEASAR skeletonization of 3D label volumes on NVIDIA GPUs

623 10 0

annotationframeworkclient

This is the python client for accessing REST APIs within the Connectome Annotation Versioning Engine.

581 43 19

bigclust2

Exploration and Analysis of Connectomics Data

230 4 0

axoden

Open-source tool for unbiased quantification of labeled axonal projections from microscopy images. Fluorophore- and species-agnostic, using Otsu thresholding. Available as a web app, standalone GUI, and Python package.

222 1 0