Metadata-Version: 2.1
Name: flybrains
Version: 0.1.0
Summary: Transforms to map between different Drosophila template brains
Home-page: https://github.com/schlegelp/navis-flybrains
Author: Philipp Schlegel
Author-email: pms70@cam.ac.uk
License: GNU GPL V3
Description: # navis-flybrains
        Transforms to map between different _Drosophila_ template brains.
        
        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 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._
        
        ```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 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](https://navis.readthedocs.io/en/latest/):
        
        ```Python
        >>> 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:
        ```Python
        >>> help(flybrains.IBN)
        ```
        
Keywords: Drosophila template registration brain navis transform
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: extras
