Petri Counter: browser-based, human-assisted enumeration of yeast colonies with reviewable separation of touching growth

Abstract

Background. Enumeration of yeast colonies from plate photographs becomes ambiguous when adjacent colonies touch or image artifacts resemble growth. We developed Petri Counter to combine inspectable automatic center detection with manual correction and preservation of review annotations.

Methods. A deterministic pipeline designed for dark colonies on pale agar runs locally in a browser without a trained model or GPU. Images are resampled to a maximum long-axis dimension of 1,400 pixels. Color-based dish localization defines an editable elliptical region, with an adjustable inset. Background correction and contrast thresholding identify candidate foreground regions. Local maxima of a smoothed distance transform propose colony centers within each connected region; separation and saddle-depth criteria suppress duplicate peaks. Size, intensity, and shape heuristics reject implausible candidates, and regions crossing the counting boundary are excluded. Users can inspect detections, adjust the dish outline, and add or remove centers. Saved submissions retain the original photograph, automatic and corrected markers, settings, self-reported reviewer names, and review scope.

Results. Synthetic regression checks recovered the specified counts for isolated circular objects, chains of two through six touching objects, a branched six-object cluster, and a tested unequal-size touching configuration. Additional checks covered empty scenes, a smooth illumination gradient, simulated dark-blue ink, and boundary exclusion. These checks establish behavior on constructed cases, not biological counting accuracy. Ten supplied plate screenshots serve as exploratory examples; expert-adjudicated reference counts and center annotations were unavailable for this report. Consequently, real-plate count error, detection precision and recall, split and merge error rates, and time savings remain unmeasured.

Conclusions. Petri Counter provides an inspectable prototype for assisted colony enumeration and collection of candidate reference annotations. Validation requires independent expert review and held-out plates spanning colony density, morphology, and acquisition conditions. Fully fused growth may not retain enough visual information to resolve individual colonies. Saved feedback does not automatically retrain the counter.