Compatible for PhenoCycle Experiment Designer (V2.1.0).

• generate_fusion_xpd: generate an .xpd file according to a given CODEX panel.

generate_fusion_xpd --param "/path/to/input_param.json"

{
  "xpd_f": "data/raw/test_final.xpd",
  "excel_f": "data/raw/codex_marker.xlsx",
  "output_f": "data/output/test_final.xpd",
  "start_well": "C1",
  "channel_1": "ATTO550",
  "channel_2": "CY5"
}

• xpd_f: path to newly created .xpd file with only BLANK wells.
• excel_f: path to .xlsx file with CODEX panel information.
• output_f: path to output .xpd file.
• start_well: well name of the start well.
• channel_1: channel name of the first piece of CODEX panel information.
• channel_2: channel name of the second piece of CODEX panel information.

• Cycle number (starts from 0)
  • (00, A) Cycle #
• The first piece of information:
  • (01, B) Cy3 (channel_1) # (markerName in .xpd)
  • (02, C) Oligo # (reporter in .xpd)
  • (03, D) CID # (barcode in .xpd)
  • (04, E) Clone # (clone in .xpd)
  • (05, F) Stock Concentration
  • (06, G) Desired Concentration
  • (07, H) Volume for 70µl
  • (08, I) msec # (exposure in .xpd)
  • (09, J) Comments
• The second piece of information:
  • (10, K) Cy5 (channel_2) #
  • (11, L) Oligo #
  • (12, M) CID #
  • (14, O) Stock Concentration
  • (15, P) Desired Concentration
  • (16, Q) Volume for 70µl
  • (17, R) msec #
  • (18, S) Comments

Only columns with # are necessary. The columns needed are select using the index of columns, so the index of columns should be correct ([index started from 0], [column name in Microsoft Excel]). For those unnecessary columns, empty columns can be used as space holders.