Fig. 1.

(a) The UI includes the left panel (red) for managing plugins and data common to the project, such as coordinate system origin and pixel width, which here has been set to $41\mu \mathrm{m}/\text{pixel}$. The right panel (blue) contains UI elements specific to a selected plugin. Here, we have the “set coordinate system” plugin in view. This plugin is used to set the origin and as the pixel width for the project. Here, we can see that for this project, the five image stacks have been selected. For each one, the anatomical location of bregma was clicked and the origin was taken as the average of all five clicks. (b) Plugins and processing steps used in a particular analysis can be selected and ordered via the Configure Pipeline window.