Recipes

Recipes

Short answers to the things people actually come here to do.

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Find the coordinates of a structure → Type its abbreviation or name, click the result, read the Label centre row on the card. See Finding Structures.

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Read from lambda instead of bregma → Frame → Origin → Zero the readout on → lambda → Turn on. Every readout in the app switches over and says lambda, not AP. See Working Frame.

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See a whole pathway at once → Click the auditory chip (or whichever system), then open the Projection view. The whole system's labels are plotted in AP × DV. See Projection and 3D.

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See what is at a coordinate I already have → Left panel → At a coordinate, type AP / ML / DV, read the ranked list. Or hit Pick on the plate and click where you are aiming. See At a Coordinate.

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Check that a structure's drawn boundary matches the real tissue → Select it, then switch the plate between Labeled and Nissl. The circle stays put, because all three sources are registered. See Reading a Plate.

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Get the approach angle between two points → Tick Measure, click both points. The readout gives the distance, the ML and DV components, and the angle from vertical. See Measuring.

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Plan an electrode track → Left panel → Plan a track, pick the target and hemisphere, set your angles, read Entry and Drive. Set your working frame first if your head is tilted — the angles are in your frame. See Planning a Track.

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Compare a tilted approach to a straight one → In the planner, the Straight down row always shows what the drive would be on a vertical dorsal approach, alongside your angled one.

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Make a figure → Set up the plate — source, grey, contrast, overlays — then SVG for editable outlines, or PNG if you want the histology in it. See Exporting.

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Get every auditory structure into a spreadsheet → Click the auditory chip, then CSV. It exports exactly what is listed. See Exporting.

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Send someone the exact view I'm looking at → Copy link. It carries the plate, structure, zoom, overlays, source, view, 3D settings, planned track and frame.

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Work on a rig computer with no internet → Download gerbil_atlas_explorer.html and double-click it. Everything is inside that one file, links included.

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Browse a level structure by structure → Set the scope strip to On plate N. The list now follows the plate slider, so walking the slider walks the anatomy.

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Find which plate a bregma value lands on → Type bregma -2.3 into the search box. It jumps to the nearest plate.