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Codex eval #7

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4c515b5
Initial edits to remedy problems identified by audit
kescobo Sep 18, 2026
da7fc3e
Fix provenance
kescobo Sep 18, 2026
1b002c0
Refine docs
kescobo Sep 19, 2026
e666bb2
fix url for deploydocs
kescobo Sep 19, 2026
c50de29
Fix docs deployment repo URL typo
kescobo Sep 21, 2026
80dc65f
Update docs with figure examples
kescobo Sep 22, 2026
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -7,7 +7,7 @@
[![Project Status: WIP](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

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.
It provides a common data model for multi-modal spatial experiments — transcripts, cell boundaries, tissue images, segmentation masks, and expression matrices — alongside provenance-aware FOV selection, lazy spatial views, a multi-FOV coordinate system graph, explicit persistence, and import support for SpatialData Zarr stores.

## Installation

Expand All @@ -22,7 +22,7 @@ Pkg.add("SpatialOmics")
using CairoMakie # load a Makie backend before plotting
using SpatialOmics

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

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