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. The bridging registrations page explains what those transforms are and how routes between spaces are chosen; this page is about installing and using them.

Install

pip3 install flybrains

The package itself is small: the transforms are downloaded separately, on request.

Quick start

import navis
import flybrains
import numpy as np

# One-off downloads -- pick the collections you need
flybrains.download_jefferislab_transforms()   # CMTK, Jefferis lab
flybrains.download_jrc_transforms()           # H5, Janelia brain
flybrains.download_vfb_transforms()           # CMTK, VirtualFlyBrain.org
flybrains.register_transforms()

points = np.array([[429536, 205240, 38400]])
navis.xform_brain(points, source='FAFB', target='JRC2018F')
# array([[241.53969657, 100.99399233,  35.96977733]])

flybrains.report() lists what is actually available to you, across both the Python and R downloads — worth running when a transform you expected is not found.

CMTK is required for some transforms

The Jefferis lab and VFB transform collections are CMTK registrations, so using them needs CMTK installed and on your PATH. The Janelia H5 transforms do not. If a transform route fails with CMTK missing, that is what it is telling you.

The FANC and BANC transforms need elastix instead.

Where next

Full documentation and the list of supported spaces: navis-org/navis-flybrains. The navis transforms tutorial covers applying them in practice.

On the R side, nat.templatebrains and nat.flybrains provide the equivalent, drawing on the same transform collections.