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:
FANC and JRCVNC2018F kindly shared by Jasper PhelpsMANC and FANCFAFB14 and FANCThere are plenty additional transforms that need to be downloaded separately (see below).
You can install flybrains from PyPI:
pip3 install flybrains
To install the dev version from Github:
pip3 install git+https://github.com/navis-org/navis-flybrains.git
In order to use the Jefferis lab or VFB transforms, you will need to have CMTK installed.
For the FANC to JRCVNC2018F transform, you will need to download
elastix and make sure that the path
to the binaries is in your PATH variable.
It's highly recommended that after install, you download the (optional) bridging transforms to map between template brains/nerve cords.
IMPORTANT: the URL for the JRC2018F <-> JRC2018M transform (JRC2018U_JRC2018M.h5)
was incorrect in flybrains version 0.2.6. If you downloaded it using that
version of flybrains you need to manually remove the file, update flybrains and
download again using a newer version.
:exclamation: If you already have downloaded these registrations via
nat.jrcbrainsand/ornat.flybrainsyou can skip this:flybrainsshould 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 between JRC brain templates
# (Saalfeld lab, Janelia Research Campus) - see docstring for details
>>> flybrains.download_jrc_transforms()
# This downloads H5 bridging transforms between JRC VNC templates
# (Saalfeld lab, Janelia Research Campus) - see docstring for details
>>> flybrains.download_jrc_vnc_transforms()
# This downloads (or updates) various CMTK bridging and mirror transforms
# generated or collated by VirtualFlyBrain.org - see docstring for details
>>> flybrains.download_vfb_transforms()
# Register the transforms - this is only necessary if you just downloaded them
# Alternatively just restart your Python session and import flybrains
>>> 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([[429536, 205240, 38400]])
>>> navis.xform_brain(points, source='FAFB', target='JRC2018F')
array([[241.53969657, 100.99399233, 35.96977733]])
Please see the transform tutorial
for navis to learn how to transform more complex data.
To check which transforms are available (either downloaded or via R) you can run this:
>>> # Generate a report - note the mix of transforms downloaded via Python and R
>>> flybrains.report()
Flybrains Status Report
=======================
Data Home: /Users/philipps/flybrain-data
CMTK registrations (Jefferis lab/VFB): 41 of 45
H5 registrations (JRC/Saalfeld lab): 3 of 8
nat regdirs
-----------
~/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
~/Library/Application Support/R/nat.jrcbrains: 0 CMTK | 5 H5 transforms
Meta data and surface meshes for the template brains/VNCs are readily accessible:
>>> flybrains.FAFB14
Template brain
--------------
Name: Full Adult Fly Brain
Short Name: FAFB14
Type: None
Sex: female
Dimensions: 165372 x 80745 x 6730 voxels
Voxel size:
x = 4 nanometers
y = 4 nanometers
z = 40 nanometers
Bounding box (nanometers):
x = 192200, y = 75853, z = 2007,
x = 853686, y = 398832, z = 271205,
Description: SSTEM volume comprising an entire female Drosophila brain was imaged at
4x4x40nm by Zheng et al. (2018) and is availabe for download at
https://temca2data.org/. The meta data and associated mesh represent
version 14 (FAFB14) of this data set.
DOI: 10.1016/j.cell.2018.06.019
Most templates come with a mesh e.g. for plotting via navis:
>>> flybrains.FAFB14.mesh
<trimesh.Trimesh(vertices.shape=(25047, 3), faces.shape=(50416, 3))>
>>> # You can pass the template object directly to navis' plotting functions
>>> navis.plot3d(flybrains.FAFB14)
0.3.0 (01/08/24):
AliasTransforms are now set to 0 (i.e. no cost)AffineTransforms are set to 0.1FAFB14 and FLYWIRE based on a new JRC2018F-FLYWIRE CMTK transform (S. Cachero, Jefferis lab)FLYWIREJRCFIB2022M; it now has .mesh, .mesh_brain, .mesh_vncFLYWIRE.mesh_whole_brain0.2.11 (23/07/24): fixed bounding box for JRCFIB2022Mraw0.2.10 (16/04/24):
JRCFIB2022M (maleCNS) <-> JRC2018M transform (via Saalfeld lab)JRCFIB2022M (maleCNS)0.2.9 (08/08/23): added MANC template brain and transform to/from JRCVNC2018M0.2.8 (02/04/23): added transform between JRCFIB2022M (maleCNS) and FLYWIRE0.2.7 (05/01/23): fixed JRC2018M <-> JRC2018U transform download0.2.6 (06/09/22): added JRC2018M <-> JRC2018U transform0.2.5 (22/05/22): added JRCFIB2022M mesh and transform to/from FAFB140.2.4 (12/05/22): added FLYWIRE template brain and landmark-based mirror transform0.2.0 (02/02/22): added VirtualFlyBrain.org's (CMTK) and Janelia's (H5) VNC transforms; renamed some download function0.1.14 (21/10/21): added FANC <-> JRCVNC2018F transform (requires Elastix and navis >=1.0.0)0.1.13 (14/10/21): add template and mirror transform for FANC0.1.12 (18/09/21): fixed directionality of Jefferis lab CMTK transforms0.1.11 (02/08/21): make downloads work if file size unknown0.1.10 (01/08/21): fix bug that led to warnings during transform registration on Windows systems0.1.9 (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: FAFB14sym0.1.7 (30/03/21): better deal with systems without nat libraries0.1.6 (25/03/21): fix bug that led to excessive recursive scanning of directories0.1.5 (03/03/21): fix bug that led to meshes not being packaged0.1.4 (24/02/21): added "hemibrain" alias for "JRCFIB2018F"; added hemibrain bounding box mesh0.1.3 (12/01/21): improved the warp mirror registration for FAFB140.1.2 (10/01/21): added a warp mirror registration for FAFB140.1.1 (06/01/21): added um (for microns) suffix to JRCFIB2018F transforms; added affine JRCFIB2018Fraw -> JRCFIB2018F -> JRCFIB2018Fum transforms0.1.0 (03/01/21): first working versionnavis-flybrains is critically based on nat.flybrains and nat.jrcbrains by Greg Jefferis
et al. for both inspiration regarding the implementation as well as template brain meta data.
If you use navis-flybrains in for your research please make sure to cite us
(see Zenodo DOI badge at the top of this page), navis and importantly the
people who generated the meshes & registrations distributed with flybrains!
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 (2020); doi: https://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
PLOS One (2018); doi: https://doi.org/10.1371/journal.pone.0236495
As reference for the VFB CMTK transforms please use:
A Systematic Nomenclature for the Drosophila Ventral Nerve Cord.
Robert Court, Shigehiro Namiki, J. Douglas Armstrong, Jana Börner, Gwyneth Card, Marta Costa, Michael Dickinson, Carsten Duch, Wyatt Korff, Richard Mann, David Merritt, Rod K. Murphey, Andrew M. Seeds, Troy Shirangi, Julie H. Simpson, James W. Truman, John C. Tuthill, Darren W. Williams, David Shepherd
Neuron (2020); doi: https://doi.org/10.1016/j.neuron.2020.08.005.
As reference for the FANC<->JRCVNC2018F transform by Jasper Phelps please use:
Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy.
Phelps JS, Hildebrand DGC, Graham BJ, Kuan AT, Thomas LA, Nguyen TM, Buhmann J, Azevedo AW, Sustar A, Agrawal S, Liu M, Shanny BL, Funke J, Tuthill JC, Lee WA
Cell (2021); doi: 10.1016/j.cell.2020.12.013
For references on individual template brains, please see their docstrings:
>>> help(flybrains.IBN)
When in doubt, feel free to open an issue to ask for advice.
FAQs
Transforms to map between different Drosophila template brains
We found that flybrains demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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