<p align="center">
<img src="https://github.com/schlegelp/navis-flybrains/blob/main/_static/flybrains_logo.png?raw=true" width="400">
</p>
[](https://doi.org/10.5281/zenodo.5515281)
# navis-flybrains
Transforms to map between different _Drosophila_ template brains. Intended to be used with [navis](https://github.com/schlegelp/navis).
This library is analogous to Greg Jefferis' [nat.templatebrains](https://github.com/natverse/nat.templatebrains), [nat.jrcbrains](https://github.com/natverse/nat.jrcbrains) and [nat.flybrains](https://github.com/natverse/nat.flybrains) for R.
`flybrains` ships with:
- meta data + surface meshes for 22 template brains and nerve cords
- an Elastix transform between `FANC` and `JRCVNC2018F` kindly shared by Jasper Phelps
- a landmark-based transform between `MANC` and `FANC`
- mirror transforms for `FAFB14` and `FANC`
There are plenty additional transforms that need to be downloaded separately (see below).
## Installation
You can install `flybrains` from PyPI:
```bash
pip3 install flybrains
```
To install the dev version from Github:
```bash
pip3 install git+https://github.com/navis-org/navis-flybrains.git
```
### External dependencies
In order to use the Jefferis lab or VFB transforms, you will need to have
[CMTK](https://www.nitrc.org/projects/cmtk/) installed.
For the FANC to JRCVNC2018F transform, you will need to download
[elastix](https://elastix.lumc.nl/index.php) and make sure that the path
to the binaries is in your `PATH` variable.
## Usage
<p align="center">
<img src="https://github.com/schlegelp/navis-flybrains/blob/main/_static/bridging_graph.png?raw=true" width="800">
</p>
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.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).
```Python
>>> 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](https://navis.readthedocs.io/en/latest/):
```Python
>>> 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](https://navis.readthedocs.io/en/latest/source/tutorials/transforming.html)
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:
```Python
>>> # 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:
```Python
>>> 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:
```Python
>>> 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)
```
## Changes
- `0.2.10` (16/04/24):
- added download for `JRCFIB2022M` (maleCNS) <-> `JRC2018M` transform (via Saalfeld lab)
- added mirror transform for `JRCFIB2022M` (maleCNS)
- dropped VFB transforms between JRC VNC templates (use Saalfeld transforms instead)
- `0.2.9` (08/08/23): added MANC template brain and transform to/from `JRCVNC2018M`
- `0.2.8` (02/04/23): added transform between `JRCFIB2022M` (maleCNS) and `FLYWIRE`
- `0.2.7` (05/01/23): fixed `JRC2018M` <-> `JRC2018U` transform download
- ~~`0.2.6` (06/09/22): added `JRC2018M` <-> `JRC2018U` transform~~ (YANKED)
- `0.2.5` (22/05/22): added `JRCFIB2022M` mesh and transform to/from `FAFB14`
- `0.2.4` (12/05/22): added `FLYWIRE` template brain and landmark-based mirror transform
- `0.2.0` (02/02/22): added VirtualFlyBrain.org's (CMTK) and Janelia's (H5) VNC transforms; renamed some download function
- `0.1.14` (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 FANC
- `0.1.12` (18/09/21): fixed directionality of Jefferis lab CMTK transforms
- `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
`navis-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.
## Citing
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](https://github.com/navis-org/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:
```Python
>>> help(flybrains.IBN)
```
When in doubt, feel free to open an [issue](https://github.com/navis-org/navis-flybrains/issues/new) to ask for advice.
Raw data
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"description": "<p align=\"center\">\n<img src=\"https://github.com/schlegelp/navis-flybrains/blob/main/_static/flybrains_logo.png?raw=true\" width=\"400\">\n</p>\n\n[](https://doi.org/10.5281/zenodo.5515281)\n\n# navis-flybrains\nTransforms to map between different _Drosophila_ template brains. Intended to be used with [navis](https://github.com/schlegelp/navis).\n\nThis library is analogous to Greg Jefferis' [nat.templatebrains](https://github.com/natverse/nat.templatebrains), [nat.jrcbrains](https://github.com/natverse/nat.jrcbrains) and [nat.flybrains](https://github.com/natverse/nat.flybrains) for R.\n\n`flybrains` ships with:\n\n- meta data + surface meshes for 22 template brains and nerve cords\n- an Elastix transform between `FANC` and `JRCVNC2018F` kindly shared by Jasper Phelps\n- a landmark-based transform between `MANC` and `FANC`\n- mirror transforms for `FAFB14` and `FANC`\n\nThere are plenty additional transforms that need to be downloaded separately (see below).\n\n## Installation\nYou can install `flybrains` from PyPI:\n\n```bash\npip3 install flybrains\n```\n\nTo install the dev version from Github:\n```bash\npip3 install git+https://github.com/navis-org/navis-flybrains.git\n```\n\n### External dependencies\nIn order to use the Jefferis lab or VFB transforms, you will need to have\n[CMTK](https://www.nitrc.org/projects/cmtk/) installed.\n\nFor the FANC to JRCVNC2018F transform, you will need to download\n[elastix](https://elastix.lumc.nl/index.php) and make sure that the path\nto the binaries is in your `PATH` variable.\n\n## Usage\n\n<p align=\"center\">\n<img src=\"https://github.com/schlegelp/navis-flybrains/blob/main/_static/bridging_graph.png?raw=true\" width=\"800\">\n</p>\n\nIt's highly recommended that after install, you download the (optional)\nbridging transforms to map between template brains/nerve cords.\n\n**IMPORTANT**: the URL for the JRC2018F <-> JRC2018M transform (`JRC2018U_JRC2018M.h5`)\nwas incorrect in `flybrains` version `0.2.6`. If you downloaded it using that\nversion of flybrains you need to manually remove the file, update flybrains and\ndownload again using a newer version.\n\n> :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).\n\n```Python\n>>> import flybrains\n\n# This downloads (or updates) various CMTK bridging and mirror transforms\n# generated or collated by the Jefferis lab - see docstring for details\n>>> flybrains.download_jefferislab_transforms()\n\n# This downloads H5 bridging transforms between JRC brain templates\n# (Saalfeld lab, Janelia Research Campus) - see docstring for details\n>>> flybrains.download_jrc_transforms()\n\n# This downloads H5 bridging transforms between JRC VNC templates\n# (Saalfeld lab, Janelia Research Campus) - see docstring for details\n>>> flybrains.download_jrc_vnc_transforms()\n\n# This downloads (or updates) various CMTK bridging and mirror transforms\n# generated or collated by VirtualFlyBrain.org - see docstring for details\n>>> flybrains.download_vfb_transforms()\n\n# Register the transforms - this is only necessary if you just downloaded them\n# Alternatively just restart your Python session and import flybrains\n>>> flybrains.register_transforms()\n```\n\nIn the future, simply importing `flybrains` is sufficient to make the\ntransforms available to [navis](https://navis.readthedocs.io/en/latest/):\n\n```Python\n>>> import navis\n>>> import flybrains\n>>> import numpy as np\n>>> points = np.array([[429536, 205240, 38400]])\n>>> navis.xform_brain(points, source='FAFB', target='JRC2018F')\narray([[241.53969657, 100.99399233, 35.96977733]])\n```\n\nPlease see the [transform tutorial](https://navis.readthedocs.io/en/latest/source/tutorials/transforming.html)\nfor `navis` to learn how to transform more complex data.\n\nTo check which transforms are available (either downloaded or via R) you can\nrun this:\n\n```Python\n>>> # Generate a report - note the mix of transforms downloaded via Python and R\n>>> flybrains.report()\nFlybrains Status Report\n=======================\nData Home: /Users/philipps/flybrain-data\n\nCMTK registrations (Jefferis lab/VFB): 41 of 45\nH5 registrations (JRC/Saalfeld lab): 3 of 8\n\nnat regdirs\n-----------\n~/Library/Application Support/rpkg-nat.templatebrains/regfolders: 41 CMTK | 0 H5 transforms\n/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nat.flybrains/extdata/bridgingregistrations: 5 CMTK | 0 H5 transforms\n/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nat.flybrains/extdata/mirroringregistrations: 5 CMTK | 0 H5 transforms\n~/Library/Application Support/R/nat.jrcbrains: 0 CMTK | 5 H5 transforms\n```\n\nMeta data and surface meshes for the template brains/VNCs are readily accessible:\n\n```Python\n>>> flybrains.FAFB14\nTemplate brain\n--------------\nName: Full Adult Fly Brain\nShort Name: FAFB14\nType: None\nSex: female\nDimensions: 165372 x 80745 x 6730 voxels\nVoxel size:\n x = 4 nanometers\n y = 4 nanometers\n z = 40 nanometers\nBounding box (nanometers):\n x = 192200, y = 75853, z = 2007,\n x = 853686, y = 398832, z = 271205,\nDescription: SSTEM volume comprising an entire female Drosophila brain was imaged at\n 4x4x40nm by Zheng et al. (2018) and is availabe for download at\nhttps://temca2data.org/. The meta data and associated mesh represent\nversion 14 (FAFB14) of this data set.\nDOI: 10.1016/j.cell.2018.06.019\n```\n\nMost templates come with a mesh e.g. for plotting via navis:\n\n```Python\n>>> flybrains.FAFB14.mesh\n<trimesh.Trimesh(vertices.shape=(25047, 3), faces.shape=(50416, 3))>\n>>> # You can pass the template object directly to navis' plotting functions\n>>> navis.plot3d(flybrains.FAFB14)\n```\n\n## Changes\n- `0.2.10` (16/04/24):\n - added download for `JRCFIB2022M` (maleCNS) <-> `JRC2018M` transform (via Saalfeld lab)\n - added mirror transform for `JRCFIB2022M` (maleCNS)\n - dropped VFB transforms between JRC VNC templates (use Saalfeld transforms instead)\n- `0.2.9` (08/08/23): added MANC template brain and transform to/from `JRCVNC2018M`\n- `0.2.8` (02/04/23): added transform between `JRCFIB2022M` (maleCNS) and `FLYWIRE`\n- `0.2.7` (05/01/23): fixed `JRC2018M` <-> `JRC2018U` transform download\n- ~~`0.2.6` (06/09/22): added `JRC2018M` <-> `JRC2018U` transform~~ (YANKED)\n- `0.2.5` (22/05/22): added `JRCFIB2022M` mesh and transform to/from `FAFB14`\n- `0.2.4` (12/05/22): added `FLYWIRE` template brain and landmark-based mirror transform\n- `0.2.0` (02/02/22): added VirtualFlyBrain.org's (CMTK) and Janelia's (H5) VNC transforms; renamed some download function\n- `0.1.14` (21/10/21): added `FANC` <-> `JRCVNC2018F` transform (requires Elastix and navis >=1.0.0)\n- `0.1.13` (14/10/21): add template and mirror transform for FANC\n- `0.1.12` (18/09/21): fixed directionality of Jefferis lab CMTK transforms\n- `0.1.11` (02/08/21): make downloads work if file size unknown\n- `0.1.10` (01/08/21): fix bug that led to warnings during transform registration on Windows systems\n- `0.1.9` (05/05/21): fixed mesh normals; fixed JRCFIB2018F units to nm and added JRCFIB2018Fum template;\n- `0.1.8` (10/04/21): add a simple symmetrization transform for FAFB: `FAFB14sym`\n- `0.1.7` (30/03/21): better deal with systems without nat libraries\n- `0.1.6` (25/03/21): fix bug that led to excessive recursive scanning of directories\n- `0.1.5` (03/03/21): fix bug that led to meshes not being packaged\n- `0.1.4` (24/02/21): added \"hemibrain\" alias for \"JRCFIB2018F\"; added hemibrain bounding box mesh\n- `0.1.3` (12/01/21): improved the warp mirror registration for `FAFB14`\n- `0.1.2` (10/01/21): added a warp mirror registration for `FAFB14`\n- `0.1.1` (06/01/21): added `um` (for microns) suffix to `JRCFIB2018F` transforms; added affine `JRCFIB2018Fraw` -> `JRCFIB2018F` -> `JRCFIB2018Fum` transforms\n- `0.1.0` (03/01/21): first working version\n\n## Acknowledgements\n`navis-flybrains` is critically based on `nat.flybrains` and `nat.jrcbrains` by Greg Jefferis\n_et al._ for both inspiration regarding the implementation as well as template brain meta data.\n\n## Citing\nIf you use `navis-flybrains` in for your research please make sure to cite us\n(see Zenodo DOI badge at the top of this page), [navis](https://github.com/navis-org/navis) and _importantly_ the\npeople who generated the meshes & registrations distributed with `flybrains`!\n\nAs reference for the Jefferis lab registrations please use:\n\n```\nThe natverse, a versatile toolbox for combining and analysing neuroanatomical data.\nA.S. Bates, J.D. Manton, S.R. Jagannathan, M. Costa, P. Schlegel, T. Rohlfing, G.S. Jefferis\neLife (2020); doi: https://doi:10.7554/eLife.53350\n```\n\nAs (partial) reference for the Saalfeld lab registrations please see:\n\n```\nAn unbiased template of the Drosophila brain and ventral nerve cord.\nJohn A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld\nPLOS One (2018); doi: https://doi.org/10.1371/journal.pone.0236495\n```\n\nAs reference for the VFB CMTK transforms please use:\n\n```\nA Systematic Nomenclature for the Drosophila Ventral Nerve Cord.\nRobert Court, Shigehiro Namiki, J. Douglas Armstrong, Jana B\u00f6rner, 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\nNeuron (2020); doi: https://doi.org/10.1016/j.neuron.2020.08.005.\n```\n\nAs reference for the FANC<->JRCVNC2018F transform by Jasper Phelps please use:\n\n```\nReconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy.\nPhelps 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\nCell (2021); doi: 10.1016/j.cell.2020.12.013\n```\n\nFor references on individual template brains, please see their docstrings:\n```Python\n>>> help(flybrains.IBN)\n```\n\nWhen in doubt, feel free to open an [issue](https://github.com/navis-org/navis-flybrains/issues/new) to ask for advice.\n",
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