Flatone
Berens Lab command-line tool that downloads mesh and skeleton data for an Eyewire II neuron via segment ID. It uses a large SAC reference set to flatten morphologies with skeliner and pywarper defaults.
Docs and repoTools
Command-line, Python, and interactive tools for working with Eyewire II data.
Morphotyper
Interactive connectome data explorer for visualizing Eyewire II cell types and mosaics.
Open MorphotyperSkeliner
Berens Lab Python package for parsing, preprocessing, and manipulating skeleton data extracted from Neuroglancer in SWC or JSON format. It includes a contact site finder between two segments.
RepoCell-Mosaics
Berens Lab Python tool for plotting and analyzing cell mosaics.
RepoPywarper
Lightweight tool for flattening neuron skeletons to correct for tissue curvature. It uses reference cells, such as SACs, to compute a transformation for other skeletons.
RepoCAVEClient
Seung Lab Python client for accessing connectomic datasets hosted via the CAVE backend, including meshes, annotations, synapses, skeletons, segmentation IDs, and extracting annotations or segments from Neuroglancer links.
Docs and repoCloudVolume
Seung Lab Python client for reading and writing volumetric data in Neuroglancer precomputed format. It is more low-level than the other tools, and most useful when you need to dive deep into volume data.
Docs and repo