Stalefish | Spatial Analysis of ISH Brain Slice Data

Stalefish is a Jupyter Notebook library. Stalefish has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Launch Stalefish with no path and press the 'e' key. You should now see a brain slice image in a window, with three sliders at the top of the window (Fig. 1A). The first task is to add or modify the points that will define the sampling curves that you'll build your 3D expression maps from. Stalefish has a concept of 'input modes' and the default mode is 'Curve mode'. In Curve mode, a mouse click will create green points to which a curve should be fit. Create 3, 4 or 5 points then press 'space'. The points should turn blue (or red). Pressing space 'locks in' a section of the curve. Repeat to create a complete, smooth curve along an anatomical feature of interest. When you are satisfied, press 'f' to fit the curve. A green fit line and yellow sample bins should appear. Sliders give control over the size and shape of the sample bins. Now move on to the next slice in the set with 'n' and draw a curve on the same anatomical feature (assuming it spans several slices). You can press 'h' to see help text detailing the key-press commands that are available. A more detailed description of the Stalefish application is available here: