flybrains 0.1.11

Transforms to map between different Drosophila template brains

navis-flybrains

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

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

flybrains ships with meta data, surface meshes for 17 template brains and a mirror transform for FAFB14. Additional transforms need to be downloaded separately (see below).

Installation

You can install flybrains from PyPI:

pip3 install flybrains

External dependencies

In order to use the Jefferis lab transforms, you will need to have CMTK installed.

Bridging transforms

It's highly recommended that after install, you download the optional bridging transforms to map between template brains.

:exclamation: 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 (see also code at the bottom).

>>> 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()

# Register the transforms - this is only necessary if you just downloaded them
>>> flybrains.register_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.

To check which transforms are available (either downloaded or via R) you can run this:

>>> # Generate a report - note the mix reg downloaded via Python and R
>>> flybrains.report()
Flybrains Status Report
=======================
Data Home: /Users/philipps/flybrain-data

Jefferis lab registrations: 41 of 41
Saalfeld lab registrations: 0 of 6

nat regdirs
-----------
/Users/philipps/Library/Application Support/rpkg-nat.templatebrains/regfolders: 41 CMTK | 0 H5 transforms
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nat.flybrains/extdata/bridgingregistrations: 5 CMTK | 0 H5 transforms
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nat.flybrains/extdata/mirroringregistrations: 5 CMTK | 0 H5 transforms
/Users/philipps/Library/Application Support/R/nat.jrcbrains: 0 CMTK | 5 H5 transforms

Documentation

Please see the transform tutorial for navis to learn how to use the data flybrains provides.

Changes

• 0.1.11 (02/08/21): make downloads work if file size unknown
• 0.1.10 (01/08/21): fix bug that led to warnings during transform registration on Windows systems
• 0.1.9 (05/05/21): fixed mesh normals; fixed JRCFIB2018F units to nm and added JRCFIB2018Fum template;
• 0.1.8 (10/04/21): add a simple symmetrization transform for FAFB: FAFB14sym
• 0.1.7 (30/03/21): better deal with systems without nat libraries
• 0.1.6 (25/03/21): fix bug that led to excessive recursive scanning of directories
• 0.1.5 (03/03/21): fix bug that led to meshes not being packaged
• 0.1.4 (24/02/21): added "hemibrain" alias for "JRCFIB2018F"; added hemibrain bounding box mesh
• 0.1.3 (12/01/21): improved the warp mirror registration for FAFB14
• 0.1.2 (10/01/21): added a warp mirror registration for FAFB14
• 0.1.1 (06/01/21): added um (for microns) suffix to JRCFIB2018F transforms; added affine JRCFIB2018Fraw -> JRCFIB2018F -> JRCFIB2018Fum transforms
• 0.1.0 (03/01/21): first working version

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)