g4x_viewer

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The files in this directory are G4X-viewer compatible representations of the dataset. They contain much of the same information as found in the raw data outputs, but with reduced fidelity to optimize performance for interactive viewing. These files are not intended for quantitative analysis and should be used only for visual exploration with the G4X-viewer. Please refer to the G4X-viewer documentation for more information.

{sample_id}_segmentation.bin

Viewer input field: UPLOAD SEGMENTATION FILE

Binary file containing cell segmentation polygons and other cell metadata. This file can be updated with new metadata using the update_bin function of G4X-helpers.

{sample_id}_run_metadata.json

Viewer input field: UPLOAD METADATA

JSON file containing much of the same information as the run_meta.json along with core metrics for the specific block (e.g. total_tissue_area_mm^2, median_transcripts_per_cell). File names match the sample ID (for example: A01_run_metadata.json).

{sample_id}_transcripts.tar

Viewer input field: UPLOAD TRANSCRIPT FILE

Tarball containing the viewer-ready transcript locations and metadata (gene names & colors). Load this into the G4X-viewer under "Upload Transcript File".

{sample_id}_multiplex.ome.tiff

Viewer input field: UPLOAD IMAGE FILE

Multi-channel OME-tiff file containing aggregated images for all protein targets as well as nuclear and cytoplasmic stains.
Note: On windows, this may appear as {sample_id}_multiplex.ome.

{sample_id}_HE.ome.tiff

Viewer input field: ADD FH&E IMAGE (Brightfield Settings)

Single-channel RGB OME-tiff file containing the fH&E image. This file should be loaded in the "Brightfield Images Settings" in the G4X-viewer.

{sample_id}_nuclear.ome.tiff

Viewer input field: UPLOAD IMAGE FILE

Multi-channel OME-tiff file containing aggregated images for the nuclear and cytoplasmic stains. In multiomics runs, these channels are also included in {sample_id}_multiplex.ome.tiff.

ome.tiff compatibility

All provided *.ome.tiff files can also be loaded into other standard ome.tiff readers, including Fiji, and napari.