root directory

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summary_{sample_id}.html

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

run_meta.json

JSON file containing global run information, such as software version, instrument ID, and platform details. It also includes the source files used for the transcript and protein panels.

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.

transcript_panel.csv

CSV file containing a full list of all probes used to demultiplex the detected features in the data.

protein_panel.csv

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