Navigation

QCAlign has a main window for viewing the histological section images, with an adjustable hierarchy panel on the left-hand side. Functionality for adjusting the appearance, spacing, and transparency of the grid and/or reference atlas overlay is located above the list of regions. Functionality for navigating between the slices is enabled in the top right-hand corner.

• The File button provides “save as”, “import” and “export” functionality.

• The View button provides “expand hierarchy”, “lock hierarchy”, and “Overview (Space)” functionality to visualize the hierarchy and provide an overview of the markers (also enabled by pressing the space bar).

• The Series button provides grid options for the whole series: “prefill grid”, “clear grid”, “reset everything”.

• The Section button provides grid options for the current section in the viewer: “prefill grid”, “clear grid” and “reset everything”.