Milume

Milume: a thinking surface for spatial omics.

A tactile, reactive widget that harnesses your scientific intuition.

Layer your data, select what catches your eye, and pick up where you left off in code.

Milume is a simple, reactive Jupyter (anywidget) surface for forming intuition about spatial omics data, which then drives the analysis that follows. The name comes from mille (thousand, as in mille-feuille, layers) + lume (light).

Tool	Role	Demo
LandmarksWidget	Draw selections and landmarks on tissue coordinates; measure from the notebook

More widgets and helpers may land here over time.

Install

pip install milume

Formerly spatial-rx

Milume was called spatial-rx. The API is unchanged; only the names moved:

pip uninstall spatial-rx
pip install milume

import milume   # was: import spatial_rx

The final spatial-rx release is a thin shim that depends on milume and re-exports it from spatial_rx with a DeprecationWarning.

Alongside other viewers

Milume complements other viewers. Use Milume to form intuition: layer images, cells, and transcripts in a notebook, select what stands out, and carry the selection straight into your analysis code. Use heavier viewers when you need to inspect in depth. Landmarks and selections round-trip as plain geometry and obs_names, so you can hand the same regions to any viewer.

From source:

uv sync --extra demo --group dev

LandmarksWidget

Draw selections and landmarks on tissue coordinates, color by category or gene, expand neighborhoods, and inspect the 3D tissue under a window.

import milume

w = milume.peek(adata, color="cell_type")   # AnnData with obsm["spatial"]
w = milume.peek(sdata, color="cell_type")   # SpatialData on disk: adds the 3D cube

From a SpatialData, the widget finds the table, the labels element it annotates, a 3D image on the same grid, and their µm frame (override with table=, image=, labels=; contrast_limits= for the image). Press I (Inspect): hovering shows a live coarse preview of the tissue under the cursor, and a click places a 300 µm window and docks a floating full-resolution cube of it, colored like the map, with your landmarks drawn on top. Save in the dock's title bar adds the window as an inspect selection to its history strip. Read the inspected cells back with w.get_obs_names(adata, "<inspect id>") or w.selections. Hold Space to pan in any tool.

Read results back in Python:

Large expression matrices are sent sparse; pass genes= to limit the gene catalog.