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Basic Usage

This tutorial covers the essential steps for launching UELer and navigating image data.

1. Launch the Viewer

After configuring your paths, run all cells in script/run_ueler.ipynb. The viewer appears inline at the bottom of the notebook.

2. Select an FOV

Use the Select Image dropdown in the left panel to choose a Field of View (FOV). UELer loads the image data on demand and caches recently accessed FOVs in memory.

The Cache Size slider controls how many FOVs can be held in memory at once. Increase it if you have sufficient RAM and want faster back-and-forth navigation.

3. Select Channels

In the Channel Selection list box, click one or more channel names to display them. Hold Shift to select a range, or Ctrl / Cmd to select individual channels.

The displayed image composites all selected channels using their assigned colors and contrast ranges.

4. Load a Marker Set

If you have previously saved a Marker Set (a named combination of channels, colors, and contrast ranges), select it from the Marker Set dropdown to restore that configuration instantly.

To save a new marker set, configure channels to your liking and use the Save marker set button.

5. Adjust Contrast and Colors

Expand the Channel accordion in the left panel. Each selected channel shows:

  • A color picker to set the display color.
  • A contrast range slider to adjust the minimum and maximum display values.

These settings are per-session. Save them as a marker set to reuse them.

6. Overlay Masks and Annotations

If masks_folder and/or annotations_folder were set:

  • Expand the Mask accordion to enable segmentation mask overlays.
  • Expand the Annotation accordion to enable annotation fills or outlines.

You can choose between outline-only, fill-only, or combined display modes, and adjust fill opacity.

7. Use the Channel Grid View

Enable Channel grid view in the Channels panel to render each visible channel as a separate labelled pane in a synchronized subplot grid. This is useful for comparing channels side by side without toggling selections.