Section registration

Use this functionality to match experimental sections with sections from an atlas and to identify anatomies from the ontology.

This functionality includes two panels: Registration controls and Atlas ontology. To toggle between panels, use the buttons on the right hand side.

Registration controls

Also see Registering sections

ClosedRegistration

Identifies the position of a complete section within the atlas by scanning along the sectioning axis.

Search locally

Identifies the position of a partial section or refines a whole brain search.

  • Make manual adjustments via Adjustment before running the local search.
  • Local search only considers section positions that are similar to the current section position.

Refinement

Optional to further refine the alignment. Nonlinear allows for warping.

ClosedAdjustment

Use manual adjustments to improve how the two sections match.

Scale

Change the scaling of the sectioning plane.

When the sliders are centered, the scale parameters are set to 1 (1 μm in the experimental section measures 1 μm in the atlas).

Shift

Adjust the position of the section within the atlas; Z refers to the sectioning axis.

When the sliders are centered, the section is placed in the middle of the atlas.

Rotations

Adjust the orientation of the section relative to the atlas; Z is perpendicular to the sectioning plane.

When the sliders are centered, the section is placed in the middle of the atlas.

ClosedVisualization

Use the Visualization options to help you visualize the overlapping sections.

To adjust transparency with the slider: the closer to Section, the more visible the experimental section; the closer to Atlas, the more transparent the experimental section.

Atlas Ontology

Also see Identifying anatomical structures

The ontology provides a comprehensive list of anatomical structures.

  • To see substructures, click the + button.
  • To find a structure in the list, use the Search bar.
  • For help in identifying search terms, hover your mouse over the reference or the experimental section; you will see the names of the corresponding anatomical areas.
  • To delineate and annotate an anatomical structure, check the corresponding box in the ontology.