Aligned Plate Widget

What this widget does

The Aligned Plate Widget loads images from multiple OMERO plates that have been spatially registered and overlays them in the Napari viewer. This is useful when the same well position was imaged across separate plates — for example, different drug treatments, time series acquired on different days, or repeated experiments — and you want to compare them side by side with the cells in the same positions.

Opening the widget

In Napari, go to Plugins → Omero Screen Napari → Aligned Plate Widget.

What you need to fill in

Field	What to enter	Example
Plate ID	The primary OMERO plate to load	3869
Well Position	A single well position	A1
Image index	Which image within the well to display	0
Sample Alignments	Tick this to display alignment reference points for verification	off

Click Enter to load.

What happens

1. The widget loads the primary plate image for the well you specified.
2. It discovers all aligned plates from the alignment data stored in OMERO or a local CSV file (agg_data.csv).
3. X/Y translation offsets are applied to each aligned plate so that cells from different plates land on the same pixel coordinates in the viewer.
4. Each fluorescence channel is added as a separate layer with an appropriate colourmap.
5. Duplicate channels (same channel name appearing in more than one plate) are filtered so the viewer is not cluttered.

Navigating the overlay

Use Napari’s standard layer controls to explore the overlay:

• Toggle individual layers on/off using the eye icon next to each layer.
• Adjust opacity sliders to blend layers visually.
• Switch between Additive and Translucent blending modes for different comparison styles.

Alignment data

Spatial alignment means that a prior analysis has calculated how much each plate’s images need to be shifted (in X and Y, in pixels) to match a reference plate. This offset data must already exist — either as an OMERO annotation or as a agg_data.csv file — before using this widget.

The pixel size from the image metadata is used to convert physical distances into pixel shifts correctly.

Tips

• Only a single well can be loaded at a time.
• Enable Sample Alignments to display the reference points used for registration, which lets you verify visually that the overlay is correct before drawing biological conclusions.
• If the overlay looks misaligned, the alignment data may have been generated with a different image size or pixel size. Check that all plates were acquired with the same objective and settings.
• Use Additive blending to see both plates’ signals simultaneously; use Translucent with reduced opacity to compare one plate against another.