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Map Mode

Map mode stitches multiple FOVs into a single spatial overview, allowing you to navigate the full tissue section as one continuous canvas.

What Is Map Mode?

In standard view, UELer loads one FOV at a time. In map mode, all FOVs are stitched together using a spatial layout descriptor. This lets you:

  • See the spatial relationship between FOVs at a glance.
  • Pan and zoom across the entire tissue without switching FOVs manually.
  • Capture and export ROIs that span multiple FOVs.

Enabling Map Mode

Map mode requires a map descriptor file that defines the physical positions and sizes of each FOV. To activate it:

  1. In the notebook, pass the path to your map descriptor when creating the viewer.
  2. Click the Map mode toggle in the viewer controls.

Once activated, the image canvas switches to the stitched composite view and the FOV selector is disabled (navigation happens by panning).

  • Pan — Click and drag the canvas to move around the stitched map.
  • Zoom — Scroll to zoom in or out.
  • Tile rendering — Only the tiles visible in the current viewport are loaded; the viewer caps the number of tiles rendered per frame to maintain responsiveness.

Large datasets

For maps with many FOVs (> 80 tiles in view), only the nearest tiles to the viewport center are rendered. Adjust the map_render_tile_limit setting in the viewer if needed.

Capturing ROIs in Map Mode

You can capture ROIs in map mode just like in standard mode. The ROI Manager stores the stitched-map coordinates alongside a [MAP:<id>] label so you can distinguish map-mode ROIs from single-FOV ROIs.

ROI thumbnails in map mode are rendered from the stitched tile layer.

Exporting ROIs in Map Mode

Batch export fully supports map-mode ROIs. When a ROI has fov="" and a non-empty map_id, the batch exporter renders the stitched region using the VirtualMapLayer and saves it with the filename prefix map_<id>_roi_<roi_id>.<format>.

See the Batch Export tutorial for more details.

Deactivating Map Mode

Click the Map mode toggle again to return to single-FOV mode. The FOV selector and all per-FOV plugin behaviors are restored automatically.