Sorting should now work for multi-shank probes without needing to vertically stack the shanks.
This release adds distance gating for universal template positions, to match the behavior of previous versions of Kilosort. By default, templates will be excluded if they are farther than `max(dmin, dminx)` microns from the nearest active site. This can be adjusted manually by changing the new `max_channel_distance` parameter in "Extra settings." Universal template placement can be previewed in the GUI by checking "Universal Templates" under the probe plot. Note that changing any of `dmin, dminx or max_channel_distance` will change the positions of the universal templates, but this will not show on the plot until you change one of the other options or click "Preview Probe" again. The probe plot also includes axes to show scale, and a "True Aspect Ratio" checkbox to switch to a physically proportional representation.
Additionally, center points for template groupings are now determined in a way that should work well for multi-shank probes, removing the need for artificially stacking shanks on top of one another. The placement of these grouping centers can also be previewed in the GUI by checking "Grouping Centers" under the probe plot. You should see one column of centers on each shank. If this is not happening, or if you're using a 2D array, you may need to specify the new `x_centers` parameter in "Extra settings."
**Full Changelog**: https://github.com/MouseLand/Kilosort/compare/v4.0.3...v4.0.4