Medaka embryo in 96 well plate - Widefield Brightfield

Bioimage Analyst

102 hpf medaka embryos in 96 well plate (4 embryo/well) - brightfield - 2X magnification - ACQUIFER Imaging Machine

Gierten, Jakob, et al. "Automated high-throughput heart rate measurement in medaka and zebrafish embryos under physiological conditions." bioRxiv (2019): 548594.

Used as benchmark dataset for Multi-Template-Matching by Thomas and Gehrig 

See implementation in Fiji

Multi-Template matching


Multi-template matching can be used to localize multiple objects using one or a set of template images.

Contrary to previous implementations that allow to use only one template, here a set of templates can be used or the initial template(s) can be transformed by rotation/flipping.

Multiple objects detection without redundant detections is possible thanks to a Non-Maxima Supression relying on the degree of overlap between detections.

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idTracker: Tracking animals


idTracker is a videotracking software that keeps the correct identity of each individual during the whole video. It works for many animal species including mice, insects (Drosophila, ants) and fish (zebrafish, medaka, stickleback). idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. Technique details and analyses of several applications are described in Pérez-Escudero et al (2014).

Video protocol:

Example image: Example video of 5 zebrafish

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