File formats

.platemap (project)

A JSON file holding the whole project: plates, well values, fields (including colors, units and auto-fill mappings), layers, figure style and platemap export settings. Being plain text, it works well with version control and can be inspected with any JSON tool.

{
  "version": 1,
  "name": "Dose-response demo",
  "plates": [
    { "id": "p1", "name": "Plate 1", "rows": 8, "cols": 12, "barcode": "BR00123456",
      "wells": { "B3": { "cell": "HepG2", "compound": "Staurosporine", "conc": 1 },
                 "B4": { "cell": "HepG2", "compound": "TGF", "conc": 10, "conc@unit": "ng/ml" } } }
  ],
  "fields": [ { "id": "conc", "name": "Concentration", "type": "number", "unit": "µM", "role": "dose", "exportName": "concentration" } ]
}

A well-level "<field>@unit" key stores a unit that differs from the field's default.

Platemap CSV (pycytominer)

One row per well with data, columns as configured. Default:

WellRow,WellCol,well_position,celltype,treatment,concentration,vehicle,compound_class,treatment_group

• well_position is zero-padded (B02).
• Numbers include their unit (10ng/ml, 1uM); vehicle is a plain 0.
• File name: platemap_<plate>.csv (pattern editable).

barcode_platemap.csv

Assay_Plate_Barcode,Plate_Map_Name
BR00123456,platemap_CP_screen_01

Data CSV

File → Export data: CSV: one row per well on every plate.

plate,well,row,column,Cell line,Compound,Concentration (µM),…
Plate 1,B3,B,3,HepG2,Staurosporine,1,…

Import

Recognized well columns: well, well_position, Metadata_Well, or WellRow + WellCol. Plate columns: plate, plate_map_name, Metadata_Plate. Delimiter (comma or tab) is detected automatically. See Saving & importing.

Figures

Format	Details
PDF	Vector, one page per plate, page size fitted to the figure
SVG	Vector, fonts as text, editable in Illustrator/Inkscape
PNG	Raster at 150–1200 dpi with the DPI recorded in the file