Resources


gunpowder

A library to facilitate machine learning on multi-dimensional images.

elmr

Provides tools to move between adult brain EM and light level data, emphasising the interaction between the CATMAID web application and the R Neuroanatomy Toolbox package.

drvid

API access to the 'DVID' (Distributed, Versioned, Image-oriented Dataservice).

nat.rcatmaid

This package provide access to the API exposed by the CATMAID (C ollaborative A nnotation T oolkit for M assive A mounts of I mage D ata) web tool.

nabor

An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D).

DotMotif

Subgraph isomorphisms on connectomes.

nat.flybrains

Includes 3D brain surfaces, bridging and mirroring registrations, and neuropil segmentations for various template brains.

kimimaro

Skeletonize Densely Labeled Images

TensorStore

C++ and Python library for efficiently reading and writing multi-dimensional arrays in formats supported by Neuroglancer.

neuroglancer converter scripts

Scripts for converting the BigBrain dataset to the Neuroglancer precomputed data format, which may serve as a useful example for converting other datasets.

pymaid

A Python-CATMAID interface. Lets you interface with CATMAID servers. Critically, it's built on top of navis and you can natively use navis functions with pymaid neurons. Note that due to a name clash the library is called python-catmaid on PyPI.

brainmaps_api_fcn

Library to interact with the Google BrainMaps API

SBEMimage

Versatile acquisition software for serial block-face electron microscopy

brainmappy

Python tools to interact with Google BrainMaps API

VFB_connect

A library for querying VFB servers (neo4j, owlery, solr)

navis-flybrains

Transforms to map between different Drosophila template brains. Intended to be used with navis.

MeshParty

Skeletonize Neuron Meshes

intern

A Python library for data access from BossDB, DVID, CloudVolume, and more.

Plugin for Blender

Plugin for Blender 3D that allows fetching data from CATMAID server for high-quality renderings.

bossphorus

A simple volumetric datastore modeled after the BossDB API.

neuprintr

Access to the neuprint connectome analysis service, including functions to fetch skeletons, synapses and ROIs, query connectivity data and develop new low level queries.

Agglomeration Proofreading

Agglomeration-Based Proofreading with Neuroglancer from Google's BrainMaps API

CBLAST

Tools for clustering neurons using synaptic connectivity

flycircuit

Functions and data for spatial analysis and annotation of neurons from the 'FlyCircuit' collection available online at http://flycircuit.tw.

nat.templatebrains

Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.

chunkflow

Compose chunk operators to create pipeline for distributed computation

skeletor

Mesh Skeleton Extraction Using Laplacian Contraction

GrandIso

Pure-python, very efficient subgraph isomorphism/monomorphism (motif-search)

mesh-deco

A Python-based utility for distributed meshing.

Grand

Drop-in scalable graph toolkit (Dask for NetworkX)

neuprint-python

A Python library to interface with the neuPrint connectome analysis service maintained by Janelia. Note that navis wraps this library and adds some convenience functions.

neuromorphr

Access to the NeuroMorpho online repository (version 7.7 ) for single-cell neuron morphology data, enabling users to easily find and use neurons from this repository with nat family packages.

Neuroglancer

Web-based volumetric data visualization

catbot

Python 3 Slack bot to interface with CATMAID server, NBLAST and Zotero. Based on Slack's Python API.

navis

Neuron Analysis and Visualization. A general purpose neuron library for visualization and analysis of neuronal morphologies. It also features interfaces e.g. with Blender 3D and the natverse via rpy2.

elektronn3

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

vfbconnectr

An R Interface to vfb-connect to query virtualflybrain.org

pyroglancer

Pythonic interface to neuroglancer for displaying neuron data

MorphX

Toolkit for exploration and segmentation of 3D morphologies.

daisy

Block-wise task scheduling for large nD volumes.

natverse

Neuroanatomical data analysis. The natverse is a collection of interoperable R packages to import, visualise, analyse, manipulate and export 3D neuroanatomical data, including neurons, brains and brain regions. It has been used to study brain and circuit organisation in species from flies to fish and mice.

nat.nblast

This R package implements the NBLAST neuron similarity algorithm

npyjs

Read numpy .npy files in JavaScript/Node.js.

SyConn

Automated synaptic connectivity inference for volume electron microscopy

fafbseg-py

Tools to work with manual and auto-segmented data in FAFB

nat - NeuroAnatomy Toolbox

An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. nat is the core package of a wider suite of neuroanatomy tools introduced at http://natverse.github.io