spatial-rx

Tools for exploring spatial omics data in notebooks — reactive widgets that stay
in sync with your Python analysis.

More widgets and helpers may land here over time.

Install

Library only:

pip install spatial-rx

From source (includes demo notebook deps and test tools):

uv sync --extra demo --group dev

LandmarksWidget

An anywidget for spatial coordinates: top tool bar, left sidebar, drawing-only synced state.

• Selections — lasso, rectangle, rotatable ellipse
• Landmarks — point, line, spline, shape
• Layer tools — spline tension; directional buffer on lines/splines (left / both / right)

Use get_mask / get_indices(selection_id=...) to restrict points. Distance, composition, gradient, and other tables belong in the notebook.

Matplotlib (static figure)

from spatial_rx import LandmarksWidget

w = LandmarksWidget(fig)
idx = w.get_indices(x, y, selection_id="selection 1")

Scatter (pan / zoom)

Interactive points use regl-scatterplot (same WebGL engine as jupyter-scatter). In Pan/Zoom mode, navigate the scatter; switch to lasso / landmark tools to draw.

from spatial_rx import LandmarksWidget

w = LandmarksWidget.from_points(x, y, color=cell_type, width=900, height=900)
w.set_color(gene_expression)  # update colors without rebuilding
idx = w.get_indices(x, y, selection_id="selection 1")

Demo

Spatial transcriptomics playground (demos/landmarks.py; data under demos/data/):

Or run locally:

git clone https://github.com/ckmah/spatial-rx.git
cd spatial-rx
uv sync --extra demo
uv run marimo edit demos/landmarks.py