regrender

Tools for 2D mouse brain registration to the Allen Common Coordinate Framework (CCF)

A napari-based Python toolkit For registering histological brain slices to the Allen Brain Atlas, annotating cells/ROIs, reconstructing probe tracks, and rendering the results with brainrender.

Features

• Interactive slice→CCF registration (regrender register) — pick landmark pairs in napari, estimate a homography/affine transform.
• ROI annotation (regrender roi) — label cells on raw images, project them into CCF space, and render.
• Probe-track reconstruction (regrender probe) — reconstruct electrode shanks from dye labels across serial sections.
• brainrender rendering of ROIs and probes in 3D atlas space.

Demo

regrender register — match landmark pairs between the atlas plane (left) and histology (right):

regrender roi — label cells per channel, then project + render in 3D with brainrender:

regrender probe — pick dye points per shank and reconstruct the tracks in 3D:

Installation

# Option 1 — one-shot CLI install, no clone or env needed (recommended for users)
uv tool install git+https://github.com/ytsimon2004/regrender.git

# Option 2 — uv virtual environment (development)
git clone https://github.com/ytsimon2004/regrender.git && cd regrender
uv venv && source .venv/bin/activate
uv pip install -e .

# Option 3 — conda environment (development)
git clone https://github.com/ytsimon2004/regrender.git && cd regrender
conda create -n regrender python=3.12 -y && conda activate regrender
pip install -e .

See the installation docs for details.

Quick Start

# Register each slice to the CCF   -> opens the registration GUI
regrender register -D <slices_dir>

# Label ROIs on raw slices        -> opens the ROI GUI
regrender roi -D <slices_dir>

# Probe tracks                        -> opens the probe GUI
regrender probe -D <slices_dir>

See the full documentation for the complete workflow.

Contact

Yu-Ting Wei - ytsimon2004@gmail.com