Welcome to regrender documentation!
====================================

**regrender** is a Python package (adapted from `allenCCF <https://github.com/cortex-lab/allenCCF>`_)
for napari-based 2D registration of histology to the Allen CCF, ROI annotation on raw images, and
brainrender reconstruction.

Features
---------------

- Interactive slice-to-atlas registration (``regrender register``).
- ROI annotation on raw images, projected into atlas space (``regrender roi``).
- Probe-track reconstruction (``regrender probe``).


Getting Started
---------------

.. toctree::
   :maxdepth: 2
   :caption: Documentation

   get_start/index