Connectomics Python Packages

edt

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

cloud-volume

Read and write Neuroglancer datasets programmatically.

zmesh

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

skeletor

Extraction of 3D skeletons from meshes.

caveclient

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

fpzip

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

kimimaro

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

compresso

Compresso: Efficient Compression of Segmentation Data For Connectomics

grandiso

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

igneous-pipeline

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

annotationframeworkclient

a service for interacting with the AnnotationFramework

connectomics

Common repository for connectomics-related libraries.

cits

CITS algorithm for inferring causality from time series data

sofima

Scalable Optical Flow-based Image Montaging and Alignment

catpy

Python client for the CATMAID API

diluvian

Flood filling networks for segmenting electron microscopy of neural tissue.

neuropull

A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.

morphvista

Plot MorphSync morphology objects easily with PyVista