Connectomics Python Packages

edt

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

connectomics

Common repository for connectomics-related libraries.

cloud-volume

Read and write Neuroglancer datasets programmatically.

fpzip

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

skeletor

Extraction of 3D skeletons from meshes.

kimimaro

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

sofima

Scalable Optical Flow-based Image Montaging and Alignment

caveclient

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

zmesh

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

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

catpy

Python client for the CATMAID API

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.

cits

CITS algorithm for inferring causality from time series data

diluvian

Flood filling networks for segmenting electron microscopy of neural tissue.

neuropull

A lightweight tool for pulling connectome networks and metadata.

morphvista

A package for managing multilayer morphology data