Tab ARMS Overlay

ARMS Overlay

Load an ARMS (or other fluorescence/brightfield) image, register it to the Xenium coordinate system using landmark-based affine registration, overlay spatial tile polygons coloured by cluster assignment, and run differential expression analysis between tile clusters. This tab is in the "Images" control panel group.

Controls

Image loading and orientation

Control	Description
Load ARMS H&E Image...	Opens a file dialog accepting .ome.tif, .tif, .tiff, .svs files.
Flip vertically	Flips the loaded image vertically.
Flip horizontally	Flips the loaded image horizontally.
H&E opacity	Slider (0–100, default 70). Controls layer transparency. Disabled until an image is loaded.

Landmark registration

The registration workflow is identical to the H&E Registration tab.

Control	Description
Add Xenium Landmark	Activates the Xenium landmark layer in "add point" mode.
Add ARMS H&E Landmark	Activates the ARMS image landmark layer in "add point" mode.
Clear All	Removes all landmarks and clears the registration affine.
Compute Registration	Computes a similarity affine from the landmark pairs. Enabled when 3 or more pairs are present. Shows per-landmark residuals in pixels and µm.
Residuals (read-only)	Text area showing registration quality after the last computation.
Save Landmarks...	Saves landmarks and affine to a JSON file. Enabled with at least one landmark.
Load Landmarks...	Restores landmarks and affine from a JSON file.

Tile overlay

Control	Description
Load GeoJSON + CSV...	Prompts for a GeoJSON file (tile boundary polygons) followed by a CSV file (tile name to cluster ID mapping). Renders tiles as a Shapes layer coloured by cluster.
Tile opacity	Slider (0–100, default 50). Disabled until tiles are loaded.
Outline only	When checked, tiles are rendered as outlines with transparent fill.
Tile edge width	Slider (1–100, default 20). Disabled until tiles are loaded.
Per-tile-cluster checkboxes	Scrollable 3-column grid of checkboxes — one per cluster. Selects which tile clusters to include in DEG analysis.

Tile DEG analysis

Control	Description
DEG method	Dropdown: "wilcoxon" or "t-test". Selects the statistical test for differential expression.
Filter by cluster	When checked, restricts DEG to cells that fall within the active Xenium cluster filter.
Run ARMS Tile DEG	Runs differential gene expression between the selected tile cluster groups.
Results (read-only)	Text area showing cells per tile cluster and top DEG genes after a run.
Export ARMS DEG CSV...	Saves DEG results to a CSV file. Enabled after a successful run.
Generate ARMS Volcano Plots...	Saves one PNG volcano plot per cluster pair to a chosen directory. Enabled after a successful run.
Select All	Selects all tile cluster checkboxes.
Deselect All	Deselects all tile cluster checkboxes.

Workflow

1. Click "Load ARMS H&E Image..." and select your image file.
2. Toggle "Flip vertically" or "Flip horizontally" if the image is mirrored.
3. Register the image to the Xenium coordinate system using at least 3 landmark pairs (same procedure as the H&E Registration tab).
4. Click "Load GeoJSON + CSV..." and supply the tile boundary GeoJSON and cluster assignment CSV files.
5. Adjust tile opacity, edge width, and "Outline only" as needed.
6. To run DEG analysis, check at least 2 tile clusters (each with at least 10 cells) and click "Run ARMS Tile DEG".
7. Inspect results in the text area. Optionally export the CSV or generate volcano plots.

Notes

• Landmarks, affine, tile data, and the ARMS image are all persisted to sdata_cached.zarr and restored automatically on the next launch.
• DEG requires at least 2 selected tile clusters, each containing at least 10 cells.
• Tile DEG results are cached to <dataset>/viewer_cache/arms_tile_deg_cache.parquet and restored on the next launch, so reopening the dataset does not mean re-running the test.