Tab Annot Distance

Annot Dist

The Annot Dist tab computes the minimum distance from each cell to the boundary of a selected annotation type, displays per-cluster distance distributions as violin, box, or strip plots, and can colour cells in the viewer by their distance value.

Controls

Control	Description
Clustering	Clustering used to group cells in the distribution plot
Annotation type	Annotation polygon type to measure distance to
Refresh annotation types	Rescans the Annotations layer; use if annotations were added after the tab was opened
Plot type	Shape of the distribution plot: violin, box, or strip
Max distance to show (µm, 0=all)	Clips the y-axis to this distance in micrometres; set to 0 to show all distances
Distance colormap	Colour map applied when colouring cells by distance (e.g. plasma)
Run Distance Analysis	Computes the minimum distance to the annotation boundary for every cell
Results area	Shows min, median, mean, and max distances overall, plus per-cluster medians
Show Plot	Renders the distribution plot; enabled after running the analysis. Also saves the figure — see the notes.
Export CSV...	Saves a table with cell coordinates, cluster assignment, and a distance_um column for each cell; enabled after running. Defaults to the filename annotation_distances.csv.
Colour cells by distance	Applies distance-based colouring to the cell labels layer using the selected colourmap; enabled after running
Clear distance colouring	Restores the previous colourmap; enabled when distance colouring is active

Workflow

1. Draw annotation polygons in the Annotations tab, or ensure existing polygons are loaded.
2. Select a Clustering and choose the Annotation type to measure distance to.
3. Click Refresh annotation types if the type does not appear in the dropdown.
4. Choose a Plot type and optionally set Max distance to show to focus on a spatial range of interest.
5. Click Run Distance Analysis.
6. Review per-cluster medians in the results area, then click Show Plot to visualise distributions.
7. Click Export CSV... to save the per-cell table.
8. Optionally click Colour cells by distance to see spatial distance gradients in the viewer; click Clear distance colouring to restore the previous display.

Notes

• At least one annotation polygon of the selected type must exist before running the analysis.
• Distance colouring is independent of other colouring modes; Clear distance colouring restores whatever colourmap was active before you applied distance colouring.
• Show Plot also writes the figure to <dataset>/plots/annot_distance.<fmt>, where the format follows Preferences → Plot format (SVG by default, PNG at 300 dpi if selected). No save dialog appears; the file is simply written.