https://www.virtualflybrain.org/docs/tools/Recent content in Tools on Virtual Fly BrainHugo -- gohugo.ioen-gbWed, 09 Sep 2026 00:00:00 +0100https://www.virtualflybrain.org/docs/tools/vfb-connect/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/vfb-connect/VFB_connect is the Python client for the databases behind Virtual Fly Brain. A single object wraps connections and canned queries across all of VFB’s open databases, so you can look up anatomy terms, resolve IDs between VFB and external resources such as CATMAID and neuPrint, retrieve connectivity, and download images without writing queries against each service yourself. If you are working with VFB data from Python, start here: most of the other tools on these pages consume data that VFB_connect can hand them.https://www.virtualflybrain.org/docs/tools/navis/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/navis/navis is the workhorse of the Python side of this toolchain. It represents neurons as skeletons, meshes or dotprops, and provides the operations you then want to perform on them: pruning and resampling, morphometrics, NBLAST similarity, plotting in 2D and 3D, and transformation between template spaces. Most of the other Python tools here produce or consume navis objects — pymaid returns CATMAID skeletons as navis neurons, neuprint-python does the same for neuPrint bodies, and flybrains plugs template-space transforms into navis.https://www.virtualflybrain.org/docs/tools/navis-flybrains/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/navis-flybrains/flybrains supplies navis with the Drosophila template brains and the transforms between them. Once it is imported, navis.xform_brain can move neurons, meshes or raw points between template spaces — FAFB to JRC2018F, hemibrain to JRC2018F, and so on — by finding a route through the registered transforms. VFB publishes its own bridging and mirroring transforms through this package, so the transform that moves a neuron inside VFB is the same one you get in your own analysis.https://www.virtualflybrain.org/docs/tools/cmtk/Wed, 09 Sep 2026 00:00:00 +0100https://www.virtualflybrain.org/docs/tools/cmtk/VFB’s registration and bridging pages describe how CMTK is used to align data to common template spaces. You do not need a local copy to use VFB itself — registration already happened before data was loaded. You need one if you want to run navis-flybrains or nat.flybrains transforms yourself, or register your own images. macOS (Apple Silicon) Paste this into a terminal. It installs CMTK under your home directory, so it needs no administrator rights and touches nothing outside its own folder — which matters on managed or institutional Macs, where you may have no admin rights at all.https://www.virtualflybrain.org/docs/tools/pymaid/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/pymaid/pymaid talks to CATMAID servers and returns neurons as navis objects, so skeletons you pull from CATMAID drop straight into the rest of the Python toolchain. VFB hosts the public CATMAID instances for several connectomics datasets — see what is available — and those are open for read-only access without a token. Install pip3 install python-catmaid Note the package name. There is an unrelated pymaid package on PyPI; installing that one will not give you this library.https://www.virtualflybrain.org/docs/tools/neuprint/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/neuprint/neuPrint is Janelia’s connectome database, hosting the hemibrain, MANC, optic-lobe and male-CNS datasets. Both language ecosystems have a client for it: neuprint-python and, on the R side, neuprintr. Either needs an authentication token, which you get by logging in to neuPrint and copying it from your account page. The datasets themselves are public; the token identifies you to the server. neuprint-python pip3 install neuprint-python import neuprint as neu client = neu.https://www.virtualflybrain.org/docs/tools/natverse/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/natverse/The natverse is a collection of interoperable R packages for working with 3D neuroanatomical data. It covers much the same ground as navis and its ecosystem does in Python, so which you reach for is usually decided by what the rest of your analysis is written in rather than by capability. The pieces you are most likely to want: nat is the core — reading, manipulating and plotting neurons and surfaces.https://www.virtualflybrain.org/docs/tools/nblast/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/nblast/VFB precomputes NBLAST scores and exposes them through the “find similar” queries on the website, so you do not need to run NBLAST yourself to use them — the NBLAST concept page explains what is covered and how to tell whether a given neuron has scores. This page is for when you want to score your own neurons, or score against a set VFB does not cover. NBLAST works on dotprops: neurons resampled into points with associated tangent vectors.https://www.virtualflybrain.org/docs/tools/elastix/Mon, 01 Jan 0001 00:00:00 +0000https://www.virtualflybrain.org/docs/tools/elastix/Most of the bridging transforms VFB and the Jefferis lab publish are CMTK registrations. The FANC and BANC transforms are not: they are elastix, so moving data into or out of those spaces needs elastix installed as well. If you are not working with FANC or BANC, you do not need this. What to install navis looks for a transformix executable on your PATH and uses the elastix lib directory that sits beside it.