Tools
Software you install and run against VFB data — what each tool is for, how to install it, a minimal example, and where its own documentation lives.
The pages here cover the software people most often use with VFB data: clients for getting data out, libraries for analysing and plotting neurons, and the registration toolkits that move data between template spaces. Each page is a quick start — what the tool is for, how to install it, enough code to confirm it works — and then points at the project’s own documentation, which is always the authoritative source.
Three neighbouring sections cover different things. VFB APIs documents the endpoints VFB itself serves, rather than third-party software that talks to them. Tutorials has the worked examples: longer, with real analyses and output. Resources lists external sites and databases to browse rather than install. Where a tool has a worked tutorial as well, its page here links to it.
Most of this toolchain is maintained by the wider Drosophila connectomics community rather than by VFB, and it splits along language lines: navis and its ecosystem in Python, natverse in R. The two overlap heavily in what they can do, so the practical question is usually which language the rest of your analysis is in.
VFB_connect
VFB's own Python client — query VFB's terms, images, connectivity and cross-references from code.
Opennavis
The core Python library for reading, analysing, transforming and plotting neurons.
Openflybrains
Template brains and bridging transforms for navis — move neurons and points between Drosophila template spaces.
OpenInstalling CMTK
The simplest way to get a local copy of CMTK, for using navis-flybrains / nat.flybrains bridging transforms outside VFB, or for registering …
Openpymaid
Python client for CATMAID, including the FAFB and other EM datasets VFB hosts.
OpenneuPrint clients
neuprint-python and neuprintr — query the hemibrain, MANC and other connectomes hosted at neuPrint.
Opennatverse
The R toolchain — nat and its companion packages for importing, transforming, comparing and plotting neurons.
OpenNBLAST
Scoring morphological similarity yourself, in navis or nat.nblast, rather than using VFB's precomputed scores.
Openelastix
The registration toolbox behind the FANC and BANC transforms — what to install, and the detail that catches people out.
Open