Data Directory Structure#

regrender works on a folder of serial section images (-D/--directory) or a single image (-I/--image). All outputs are written next to the input images. A typical folder looks like this after running the full pipeline:

<slices_dir>/
    ├── <stem>.tif                       # input histology slices (one per section)
    │
    ├── transformations/                 # created by `regrender register`
    │     ├── <stem>_transform.json      # registration metadata (see below)
    │     ├── <stem>_transformed.tif     # histology warped into atlas space
    │     └── <stem>_overlay.png         # histology + boundaries, outside the brain transparent
    │
    ├── roi/                             # created by `regrender roi`
    │     ├── roi_points_raw.csv         # ROIs in raw pixel coords
    │     └── roi_points_ccf.csv         # ROIs projected into CCF (after "Project")
    │
    └── probe_shanks.csv                 # created by `regrender probe`

Registration metadata — <stem>_transform.json#

Written by regrender register and consumed by roi / probe. Fields:

Field

Meaning

matrix

3×3 homography (or affine) mapping the resized slice onto atlas-plane pixels.

plane

Cutting plane (coronal / sagittal).

resolution

Atlas resolution in µm (default 10).

slice_index

Atlas plane index (voxel) the slice was matched to.

dw / dh

Cutting-plane tilt offsets.

rotate

In-plane rotation (degrees) applied to the raw slice.

flip_lr / flip_ud

Whether the raw slice was flipped before registration.

contrast

(lo, hi) contrast window used for the saved .tif, or null.

slice_xy / atlas_xy

The matched landmark point pairs (slice pixels / atlas pixels).

The rotate / flip_lr / flip_ud fields record the preprocessing so raw ROI points can be replayed into atlas space (raw → flip → rotate → resize → apply matrix).

ROI CSVs — roi/#

roi_points_raw.csv (from labeling on raw images):

  • slice — source slice stem

  • x, y — ROI position in raw image pixels

  • raw_h, raw_w — raw image shape (needed to replay the transform)

  • channel — merge / R / G / B

roi_points_ccf.csv (after “Project + Render” or roi --project) adds:

  • AP_location, DV_location, ML_location — bregma-relative CCF coordinates (mm)

  • region — Allen region acronym at that point

  • source — source slice stem

  • channel

Probe CSV — probe_shanks.csv#

From regrender probe:

  • ap_mm, dv_mm, ml_mm — bregma-relative CCF coordinates (mm)

  • probe_idx — shank index

  • point — dorsal (superficial) or ventral (deep)

  • source — source slice stem the point was picked on

The Region profile plot button also writes probe_region_profile.pdf and probe_region_profile.csv (one row per region span per shank: shank, region, extrapolated, dv_start_mm, dv_end_mm, depth_start_mm, depth_end_mm, length_mm).