SpatialOmics.jl

A Julia library for loading, representing, and analysing spatial transcriptomics data. It provides a common data model for multi-modal spatial experiments — transcripts, cell boundaries, tissue images, segmentation masks, and expression matrices — alongside lazy spatial views, a multi-FOV coordinate system graph, and SpatialData OME-Zarr interoperability with Python tools.

Installation

using Pkg
Pkg.add("SpatialOmics")

Quick start

using CairoMakie   # load a Makie backend before plotting
using SpatialOmics

# Load from SpatialData OME-Zarr (Xenium, CosMx, Visium, …)
ds = read(SpatialDataZarr(), "/path/to/experiment.zarr")

ext = SpatialExtent(4000.0, 5000.0, 1000.0, 2000.0; coord_system="global")
roi = view(ds, ext)

# Build a composite panel using standard Makie verbs
fig = Figure(size=(600, 600))
ax  = Axis(fig[1, 1]; aspect=DataAspect(), yreversed=true)
heatmap!(ax, images(roi, "morphology_focus"); channel=1, colormap=:grays)
poly!(ax,    shapes(roi, "cell_boundaries");  color=:transparent, strokecolor=:cyan)
scatter!(ax, points(roi, "transcripts");      markersize=1, color=(:red, 0.3))
tightlimits!(ax)
fig

See the documentation for a full API reference, explanations of the data model and coordinate system graph, and platform-specific guides.