Getting Started

Typical workflow

The commands are usually run in this order on a folder of serial sections (-D <slices_dir>):

1. regrender roi — label cells/ROIs on the raw slices (raw pixel coords, no registration needed yet).

2. regrender register — register each slice to the Allen CCF.

3. regrender roi --project --render — project the labelled ROIs into CCF space and render.

4. regrender probe — (optional) reconstruct probe/electrode tracks from dye labels on the registered slices.

ROIs are marked before registration but projected after it, because the saved transform is what maps raw pixels into atlas space.

Contents

• Installation
  • Prerequisites
  • Option 1 — One-shot install with uv (no environment)
  • Option 2 — uv virtual environment (development)
  • Option 3 — conda environment (development)
  • Verification
  • Download the atlas
• Slice Registration (regrender register)
  • Workflow
  • Options
• ROI Annotation (regrender roi)
  • Labeling
  • Projecting & rendering
  • Options
• Probe-Track Reconstruction (regrender probe)
  • Workflow
  • Options
• Data Directory Structure
  • Registration metadata — <stem>_transform.json
  • ROI CSVs — roi/
  • Probe CSV — probe_shanks.csv