navis-fishbrains

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

Currently fishbrains ships with:

• a brain mesh + mirror transform for the Fish2 dataset (FishEM, Janelia)

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

Installation

pip install fishbrains

To get the bleeding-edge version from Github:

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

External dependencies

Note

At this point none of the transforms in fishbrains require external dependencies. So for now these external dependencies are nice-to-have but not actually necessary.

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 fishbrains

# Plot the Fish2 brain shell mesh
navis.plot3d(fishbrains.Fish2)

# Mirror spatial data (e.g. skeletons)
mirrored = navis.mirror_brain(skeletons, template="Fish2", mirror_axis="y")

Changes

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