g4x-viewer.zarr
The g4x-viewer.zarr directory is a G4X-viewer compatible Zarr store. It contains optimized representations of images, cell metadata, cell polygons, transcript locations, and summary content for interactive visualization.
These files are intended for visual exploration with the G4X-viewer, not as the primary source for quantitative analysis. For analysis workflows, use the raw images, transcript tables, masks, and single_cell_data files documented in this section.
images
Zarr groups containing multiscale image pyramids for the multiplex image stack and fH&E image. The multiplex image includes nuclear and cytoplasmic stain channels, plus protein channels in multiomics runs.
cells
Zarr groups containing segmentation-specific cell metadata, polygon vertices, expression matrix indices, protein intensities, UMAP coordinates, and cluster labels. The default segmentation group is
g4x_default_segmentation.
transcripts
Tiled Zarr groups containing viewer-ready transcript coordinates, cell assignments, and gene identifiers.
misc
Additional viewer assets, including
summary.htmlwhen a sample summary report is available.
metadata updates
The G4X-helpers viewer commands can export and import metadata for images, cells, and transcripts in an existing g4x-viewer.zarr store.