Capture Visualiser

A napari plugin for overlaying spatial transcriptomics capture areas onto brain sections. Compare platforms such as Xenium, Visium HD, MERSCOPE, and GeoMx by browsing Allen mouse brain atlas coronal sections and positioning scaled rectangles to see which brain regions fit within each capture area.

Features

• BrainGlobe atlases: Load any atlas from brainglobe-atlasapi (mouse, human, rat, zebrafish, etc.)
• AP plane slider: Step through coronal sections to find the plane of interest
• Capture area overlays: Rectangles scaled to platform dimensions (Xenium, Visium HD, MERSCOPE, GeoMx, BARseq)
• Interactive placement: Select, translate and rotate capture areas using napari's shape tools
• Multiple capture areas: Add several rectangles with different colours; select one to resize with presets

Installation

Option 1: Conda environment (recommended)

# From the project directory
cd capture_visualiser
conda env create -f environment.yml
conda activate capture-visualiser

This creates a conda environment and runs pip install -e . to install the package and its dependencies from pyproject.toml.

If you already have the environment and see "No Qt bindings could be found", install PyQt:

conda activate capture-visualiser
conda install -c conda-forge pyqt

Option 2: pip (existing environment)

pip install -e .

Requirements

• Python ≥ 3.11
• napari ≥ 0.6.1
• brainglobe-atlasapi ≥ 2.2.0

The Allen atlas is downloaded automatically on first use. The conda environment includes PyQt for napari's GUI.

Usage

Launching the plugin

1. Start napari:

   napari

2. Open the Capture Visualiser widget:

   • Plugins → Capture Visualiser → Capture Visualiser
   • Or use the napari Plugins menu and search for "Capture Visualiser"

Workflow

1. Load atlas
   Select an atlas from the dropdown (default: allen_mouse_25um, recommended for mouse) and click Load atlas. Atlases marked "(recommended)" are suggested starting points. A download progress bar appears when installing a new atlas. You can switch to another atlas at any time—capture areas are preserved and repositioned in the new atlas space.

2. Browse AP planes
   Use the AP plane slider to move through coronal sections and find the region you care about.

3. Use presets
   Click a preset button (Xenium, Visium HD, MERSCOPE, GeoMx, BARseq) to resize the selected capture area. Hover for a short description. Select a shape first with the Select shapes tool.

4. Custom capture area
   Enter width and height in mm, then click Apply to resize the selected capture area.

5. Multiple capture areas
   Click Create a new capture area to add another rectangle. Each new area gets a different colour. Select any shape to resize it with presets or Apply.

6. Position the capture rectangles
   Use napari's Select shapes tool to move and rotate rectangles over the atlas. Select one to make it the target for preset/Apply resize.

7. Rotate
   Click Rotate current capture area 90° to rotate the selected rectangle.

Tips

• Keep the viewer in 2D mode for coronal browsing.
• Use napari's built-in dimension slider in addition to the plugin slider if you prefer.
• You can toggle layer visibility (reference vs annotation) in the napari layer list.

Configuration

Setting	Description	Default
Width (ML)	Capture area width in mm	10.45 (Xenium)
Height (DV)	Capture area height in mm	22.45 (Xenium)
Atlas	Dropdown selection from brainglobe-atlasapi	allen_mouse_25um (default)
Presets	Config file	presets.json in package; override at ~/.config/capture_visualiser/presets.json

License

BSD-3-Clause

Acknowledgements

• BrainGlobe for brainglobe-atlasapi and the Allen atlas integration
• brainrender-napari for atlas visualisation patterns in napari
• napari for the viewer and plugin system