5. Selecting regions of interest
Localize regions of interest in the reference atlas
Now, you have registered your slices and can scroll through them by pressing the left arrow on the AtlasViewer and pressing 'a' to see the brain-region boundaries. (If you did not do this, ROI selection can still work. For example, you can use the simpler allenAtlasBrowser function (see Navigating in the reference atlas) or you can just save atlas positions in the AtlasTransformBrowser without registering the slices.)
Before running Navigate_Atlas_and_Register_Slices.m, fill in the parameter probe_save_name_suffix = 'electrode_track_1' with a name to be attached to the ROIs you mark and save.
Press 'p' to toggle probe point mode. Now, clicks will show up on the AtlasViewer as points tagging your ROI - in the example shown below, a fluorescent track marking an electrode insertion. In the optimal use case, you will be scrolling between slices (the left arrow key function). In this case, probe points will show up only on the registered slice on which they were clicked (as in the example below). If using the simple allenAtlasBrowser, however, all clicked points will remain visible.
A window called the Transformed Slice & Probe Point Viewer will appear while marking points. When this figure is selected, pressing left and right will move through the slice images and show you previously clicked points. This can be helpful in an experiment with several electrodes, when trying to figure out which fluorescent blob corresponds to which probe. It can also be ignored.
Press 'n' to add a new probe in a new color. Press 'p' to switch between which probe you are marking (the console will then report which probe is selected). Press 'd' to delete the most recently clicked point from the selected probe. Press 's' to save the clicked points for analysis.
