xenLite zarrlook – early probe of R/zarr interactions

Vincent J. Carey, stvjc at channing.harvard.edu

September 18, 2024

Source: vignettes/zarrlook.Rmd

Introduction

This document is a very rough and ready illustration of a way of interacting with a Zarr store of a Xenium experiment.

To produce the store, I followed the spatialdata sandbox script to produce a 6.6GB data.zarr (renamed to lungdata.zarr).

Once this store is ready, we can use reticulate to explore the store using spatialdata and other modules. As use cases emerge, we may organize these approaches with basilisk.

This document can be re-computed as long as reticulate can import spatialdata, spatialdata_plot, and matplotlib.pyplot. EBImage should also be installed from Bioconductor. Follow the sandbox script to produce data.zarr, then rename.

The data layout 

library(reticulate)
sda = import("spatialdata")
sda$read_zarr("lungdata.zarr")

After a python warning, we have

SpatialData object, with associated Zarr store: /home/vincent/XEN_ZARR/lungdata.zarr
├── Images
│     ├── 'he_image': DataTree[cyx] (3, 45087, 11580), (3, 22543, 5790), (3, 11271, 2895), (3, 5635, 1447), (3, 2817, 723)
│     └── 'morphology_focus': DataTree[cyx] (5, 17098, 51187), (5, 8549, 25593), (5, 4274, 12796), (5, 2137, 6398), (5, 1068, 3199)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (17098, 51187), (8549, 25593), (4274, 12796), (2137, 6398), (1068, 3199)
│     └── 'nucleus_labels': DataTree[yx] (17098, 51187), (8549, 25593), (4274, 12796), (2137, 6398), (1068, 3199)
├── Points
│     └── 'transcripts': DataFrame with shape: (<Delayed>, 11) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (162254, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (162254, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (156628, 1) (2D shapes)
└── Tables
      └── 'table': AnnData (162254, 377)
with coordinate systems:
    ▸ 'global', with elements:
        he_image (Images), morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)

Visualizing a patch 

library(xenLite)
nn = rast_zarr("lungdata.zarr")
ii = EBImage::Image(nn, colormode="Color")
EBImage::display(ii, method="browser") # to browser for zoom/pan