Create a metadata template for matched treatment-control sets

Writes one row per image. Treatment, set and optional annotations may remain blank for image measurement. For comparisons, controls use the treatment label control; set_id decides which controls belong to which treatments. The same treatment label across sets must represent the same intervention. See validate_metadata(). Review experimental assignments and image masks before interpretation. No metadata approval flag is generated or required. Image QC warns by default; no review-flag edits are needed for the standard workflow. Standard optional fields (fungus, zymo_strain, medium, day, replicate, photo_date and notes) are included even when unrecorded. Custom columns supplied through extra are retained.

Usage

make_metadata(
  dir,
  file = file.path(dir, "plate_metadata.csv"),
  treatment = NA_character_,
  set_id = NA_character_,
  patterns = NULL,
  extra = list(),
  overwrite = FALSE,
  recursive = FALSE
)

Arguments

dir: Folder with photographs.
file: Output CSV path.
treatment: Optional default treatment label.
set_id: Optional default set ID; leave missing for multiple sets.
patterns: Optional named regular expressions for treatment labels.
extra: Named list of additional metadata columns.
overwrite: Whether to replace an existing template.
recursive: Search nested image folders. Relative paths distinguish repeated basenames.

Value

Metadata invisibly, also written as CSV. Experimental assignments are needed only for matched comparisons; optional annotations may remain blank.