Fig. 2

Multi-template matching and Non-Maxima Suppression for the detection of randomly oriented and positioned medaka embryos. a Image in which the search is performed (2048 × 2048 pixels - scale bar: 1 mm) and template as inset (400 × 414 pixels). The search was performed with a set of templates (original template, vertical and horizontal flip, each rotated by 90°, 180° and 270°). Parameters for the detection: score type: 0-mean normalized cross-correlation, N = 4 expected objects per image, score threshold: 0.35, maximal overlap between bounding boxes: 0.25. b One of the derived correlation maps from A: red crosses indicate possible local maxima before Non-Maxima Suppression (NMS). The grid area indicates the smaller size of the correlation map compared to the image in which the search is performed as explained in Additional file 13. c Bounding boxes associated to the maxima shown in b and overlaid on the searched image. Colours are highlighting overlapping bounding boxes. The bounding box dimensions are identical to the dimensions of the template used for the search. d, e Preventing overlapping detections by NMS. Shown are 2 overlapping bounding boxes predicting possible object locations. Each predicted location is associated to a probability score S to contain an object. The ratio between the intersection (d) and the union (e) area of the bounding boxes (Intersection over Union or IoU) is computed to decide whether the 2 overlapping bounding boxes are likely to predict the location of the same object (IoU close to 1) or the locations of distinct objects that are close to each other (IoU close to 0). For a detailed description of Non-Maxima Suppression see Additional file 13. f Yielded object detections after NMS with a maximal IoU of 0.25, to return the N_objects = 4 best detections