ASTEC stands for Adaptive Segmentation and Tracking of Embryonic Cells. It proposes a full workflow for time lapse light sheet imaging analysis, including drift/motion compensation before the segmentation itself, and the capacity to correct for it.  It was used to process 3D+t movies acquired by the MuViSPIM light-sheet microscope in particular.

Astec embryon

Medaka embryo in 96 well plate - Widefield Brightfield

Submitted by LThomas on Mon, 04/29/2019 - 12:18

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 https://github.com/LauLauThom/MultipleTemplateMatching


Quantitative Criterion Acquisition Network (QCA Net) performs instance segmentation of 3D fluorescence microscopic images. QCA Net consists of Nuclear Segmentation Network (NSN) that learned nuclear segmentation task and Nuclear Detection Network (NDN) that learned nuclear identification task. QCA Net performs instance segmentation of the time-series 3D fluorescence microscopic images at each time point, and the quantitative criteria for mouse development are extracted from the acquired time-series segmentation image. The detailed information on this program is described in our manuscript posted on bioRxiv.

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