Figure 6.

Annotating labels in the Atlas Editor. (A) Opening the sample brain in MagellanMapper initially shows the bottom z-plane in the ROI Editor. (B) Scrolling a mouse moves the overview plots’ z-plane, while clicking on the plot moves the ROI offset controls to that position and shows a preview of the ROI (dashed box). Opening the image adjustment tab (red arrow) allows brightness and contrast control. (C) Opening the Atlas Editor tab (purple arrow) shows a simultaneous orthogonal viewer of the sample brain. Scrolling through the horizontal (axial, z, or xy-plane) plane or clicking/dragging its slider (orange arrow) moves through these planes. Clicking within the plane moves the crosshairs (red arrow) and shifts the coronal (y, or xz-plane; blue arrows) and sagittal (x, or yz-plane; yellow arrows) views to the planes corresponding to these crosshair lines. (D) The Allen Developing Mouse Brain E18.5 atlas is shown with the specified labels (blue arrow) overlaid on the microscopy intensity image. Each distinct label color corresponds to a separate label in the Allen ontology. Hovering over a given label identifies its name and Allen ID (red arrow). The tools at the bottom of the editor (green arrow) allow label display adjustment as well as edit controls for painting labels in each 2D plane. (E) Example y-plane before editing, showing jagged label edges. The white bordered ellipse shows the paint brush (red arrow), whose size can be adjusted using the bracket keys. (F) The red (red arrow) and green (green arrow) regions have been smoothed by simply dragging the brush along the label borders. (G) Example edge interpolation to smooth a label edge. Painting successive planes in 2D can lead to jagged edges when viewed in the third dimension. To paint smoothly in 3D, the label fill tool (green arrow section in part D) interpolates label edits between two separate planes. The alar prethalamus (purple label) shows jagged artifacts in each plane, including irregularity between each plane (left). The anterior edge of the label has been edited in the top and bottom planes to smooth the jaggedness (middle), without touching the middle four planes. Applying the edge interpolation applies the edits from the two manually edited planes smoothly along these unedited planes. After edits, the image can be saved (green arrow section in part D).