navis-mousebrains

Transforms and meta data to map between different mouse template brains. This package is intended to be used with navis and is analogous to navis-flybrains.

Currently mousebrains ships with:

• meta data and surface mesh for the Allen CCF mouse brain template
• transforms between the CA3 EM and uCT volume by Z. Zheng (Princeton) and the Allen CCF

Installation

You can install mousebrains from PyPI:

pip3 install mousebrains

To install the dev version from Github:

pip3 install git+https://github.com/navis-org/navis-mousebrains.git

External dependencies

In order to use CMTK-based transforms, you will need to have CMTK installed.

For the Elastix-based transforms, you will need to download elastix and make sure that the path to the binaries is in your PATH variable.

Usage

import navis
import mousebrains

# Transform some points from the Zheng CA3 dataset to Allen CCF space
points = np.array([[47056, 51152, 2128]])

points_xf = navis.xform_brain(
    points,
    source="Zheng_CA3_EMraw",  # EM voxel space (18x18x45nm)
    target="AllenCCF"  # Allen CCF space (microns)
)

Changes

• 0.0.4:
• flipped Zheng CA3 uCT -> CCF transforms onto right hemisphere
• added templates for Zheng CA3 EM and uCT datasets
• 0.0.3: added transforms for the Zheng CA3 dataset

Acknowledgements

TODO

Citing

TODO

When in doubt, please open an issue to ask for advice.