How to show your own histology in the Slice figure

This guide shows you how to display your registered histology images behind the trajectory, instead of only the Allen template and annotation.

Prerequisites

  • Histology registered to the 25 µm Allen atlas, saved as NRRD or TIFF volumes with these dimensions:

    Format

    Dimensions

    NRRD

    [voxels in AP, voxels in DV, voxels in ML]

    TIFF (.tif or .tiff)

    [voxels in ML, voxels in DV, voxels in AP]

Steps

  1. Put the volumes in one folder. Name them so the GUI can tell the channels apart:

    Format

    Red channel

    Green channel

    NRRD

    RD in the file name

    GR in the file name

    TIFF

    RD or C1 in the file name

    GR or C0 in the file name

    For TIFFs, if you don’t want to name the channels by colour, call them C0 and C1 instead. The name only sets the entry in the Slice Plots menu: C0 appears as Histology green and C1 as Histology red.

  2. Add the folder as the histology dataset in the session YAML. Histology is usually shared by all the probes of an animal, so it is convenient to put it in defaults:

    defaults:
  histology:
    path: /path/to/histology

    When opening a data folder instead of a YAML, put the volumes in that folder.

  3. Load the session and cycle through the slice images with Alt+4. Each volume adds a Histology red or Histology green entry.

If both NRRD and TIFF files are in the folder, only the NRRD files are used.