navis-mousebrains

Transforms and meta data to map between different mouse template brains and coordinate systems. 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
• a transform from Allen CCF to stereotaxic coordinate system from Perens et al., 2023

Want to see more transforms or meshes included? Please open an issue.

Installation

You can install mousebrains from PyPI:

pip install mousebrains

To install the dev version from Github:

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

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

# Define a point in Zheng CA3 EM raw voxel space (18x18x45nm)
points = np.array([[47056, 51152, 2128]])

# Transform point Allen CCF (v3) space
points_ccf = navis.xform_brain(
    points,
    source="Zheng_CA3_EMraw",  # EM voxel space (18x18x45nm)
    target="AllenCCF"  # Allen CCF space (microns)
)

# Transform the points from Allen CCF space to stereotaxic coordinates
points_st = navis.xform_brain(
    points_ccf,
    source="AllenCCF",  # Allen CCF space (microns)
    target="Stereotaxic"  # Stereotaxic coordinate space (millimeters)
)

Changes

• 0.0.5:
  • added CCF -> Stereotaxic coordinates look-up from Perens et al., 2023
  • small fix for Zheng CA3 EM -> uCT transform
• 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

References

If you use navis-mousebrains in your research, please make sure to cite the people who generated the meshes & transforms distributed with mousebrains!

As reference for data related to Allen Common Coordinate Framework (CCFv3) please cite:

Wang, Q., Ding, S.-L., Li, Y., Royall, J., Feng, D., Lesnar, P., Graddis, N., Naeemi, M., Facer, B., Ho, A., Dolbeare, T., Blanchard, B., Dee, N., Wakeman, W., Hirokawa, K. E., Szafer, A., Sunkin, S. M., Oh, S. W., Bernard, A., … Ng, L. (2020). The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell, 181(4), 936-953.e20. https://doi.org/10.1016/j.cell.2020.04.007

As reference for transforms to/from the Zheng CA3 dataset please cite:

Zheng, Z., Park, C., Hammerschmith, E. W., Lu, R., Yu, S.-C., Sorek, M., Silverman, B., Jordan, C. S., Sterling, A. R., Silversmith, W. M., Collman, F., Seung, H. S., & Tank, D. W. (2025). Connectomic reconstruction from hippocampal CA3 reveals spatially graded mossy fiber inputs and selective feedforward inhibition to pyramidal cells. bioRxiv. https://doi.org/10.1101/2025.07.09.663979

As reference for the CCF → stereotaxic coordinate transform please cite:

Perens, J., Salinas, C. G., Roostalu, U., Skytte, J. L., Gundlach, C., Hecksher-Sørensen, J., Dahl, A. B., & Dyrby, T. B. (2023). Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System. Neuroinformatics, 21(2), 269–286. https://doi.org/10.1007/s12021-023-09623-9

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