root directory

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sample.g4x

JSON file containing sample and run metadata, including sample identity, instrument information, flow cell position, panel references, software version, and output schema version.

samplesheet.csv

CSV file containing detailed run information, including operator, experimental design, run parameters, flow cell layout, tissue type, and panels used. Also specifies the position of each tissue section on the flow cell.

summary_*.html

HTML file which gives a high level overview of the experiment outputs, data quality, and performance for the specific sample.

transcript_manifest.csv

CSV file containing the transcript probe manifest used to demultiplex detected features. The manifest includes probe identifiers, gene names, panel annotations, and probe type annotations.

protein_panel.csv

CSV file containing a full list of all targeted proteins in this experiment and the panel type (standard, addon).