Metadata-Version: 2.4
Name: regrender
Version: 0.1.0
Summary: 2D mouse brain registration, ROI/Probe annotation, and brainrender reconstruction
Project-URL: Homepage, https://github.com/ytsimon2004/regrender
Project-URL: Repository, https://github.com/ytsimon2004/regrender
Project-URL: Documentation, https://regrender.readthedocs.io
Author-email: Yu-Ting Wei <ytsimon2004@gmail.com>
License-Expression: MIT
License-File: LICENSE
Keywords: allen-ccf,brain-atlas,brainrender,napari,neuroscience,registration
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.12
Requires-Dist: argclz>=1.0.1
Requires-Dist: imageio
Requires-Dist: napari[pyqt5]
Requires-Dist: neuralib-atlas[brainrender]>=0.7.3
Requires-Dist: rich
Provides-Extra: doc
Requires-Dist: pydata-sphinx-theme; extra == 'doc'
Requires-Dist: sphinx; extra == 'doc'
Requires-Dist: sphinx-copybutton; extra == 'doc'
Provides-Extra: lint
Requires-Dist: mypy; extra == 'lint'
Requires-Dist: ruff; extra == 'lint'
Provides-Extra: test
Requires-Dist: pytest; extra == 'test'
Description-Content-Type: text/markdown

# 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):

<img src="docs/source/_static/register.png" alt="register" width="800">

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

<img src="docs/source/_static/roi.png" alt="roi" width="800">

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

<img src="docs/source/_static/probe.png" alt="probe" width="800">


## Installation

```bash
# 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](https://regrender.readthedocs.io/en/latest/get_start/installation.html) for details.

## Quick Start

```bash
# 1. label ROIs on raw slices
regrender roi -D <slices_dir>

# 2. register each slice to the CCF
regrender register -D <slices_dir>

# 3. project ROIs to CCF + render  (or use the GUI "Project + Render" button)
regrender roi --project --render -D <slices_dir>

# probe tracks
regrender probe -D <slices_dir>
```

See the [full documentation](https://regrender.readthedocs.io) for the complete workflow.

## Contact

**Yu-Ting Wei** - ytsimon2004@gmail.com
