flybrains 0.1.0

Transforms to map between different Drosophila template brains

navis-flybrains

Transforms to map between different Drosophila template brains.

This library is analogous to Greg Jefferis' nat.templatebrains, nat.jrcbrains and nat.flybrains for R.

flybrains ships with meta data and surface meshes for 17 template brains.

It's highly recommended that after install, you download the optional bridging registrations.

If you already have downloaded these registrations via nat.jrcbrains and/or nat.flybrains you can skip this: flybrains should be able to find the registrations downloaded via R and register them for you.

>>> import flybrains

# This downloads (or updates) various CMTK bridging and mirror transforms
# generated or collated by the Jefferis lab - see docstring for details
>>> flybrains.download_jefferislab_transforms()

# This downloads h5 bridging transforms generated by the Saalfeld lab (Janelia)
# - see docstring for details
>>> flybrains.download_saalfeldlab_transforms()

In the future, simply importing flybrains is sufficient to make the transforms available to navis:

>>> import navis
>>> import flybrains
>>> import numpy as np
>>> points = np.array([[0, 0, 0]])
>>> navis.xform_brain(points, source='FAFB', target='JRC2018F')

On import of flybrains, these data sources are injected into and can be readily used to e.g. transform 3d coordinates between brain spaces.

Acknowledgements

Critically based on nat.flybrains and nat.jrcbrains by Greg Jefferis et al. for inspiration for the implementation and meta data on e.g. template brains.

As reference for the Jefferis lab registrations, please use:

The natverse, a versatile toolbox for combining and analysing neuroanatomical data.
A.S. Bates, J.D. Manton, S.R. Jagannathan, M. Costa, P. Schlegel, T. Rohlfing, G.S. Jefferis
eLife. 9 (2020) e53350. doi:10.7554/eLife.53350.

As (partial) reference for the Saalfeld lab registrations, please see:

An unbiased template of the Drosophila brain and ventral nerve cord.
John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
bioRxiv 376384; doi: https://doi.org/10.1101/376384

For references of individual template brains, please see their docstrings:

>>> help(flybrains.IBN)