zebrafish

BACKGROUND: Zebrafish is a widely used model organism for studying heart
development and cardiac-related pathogenesis. With the ability of surviving
without a functional circulation at larval stages, strong genetic similarity
between zebrafish and mammals, prolific reproduction and optically transparent
embryos, zebrafish is powerful in modeling mammalian cardiac physiology and
pathology as well as in large-scale high throughput screening. However, an
economical and convenient tool for rapid evaluation of fish cardiac function is
still in need. There have been several image analysis methods to assess cardiac
functions in zebrafish embryos/larvae, but they are still improvable to reduce
manual intervention in the entire process. This work developed a fully automatic
method to calculate heart rate, an important parameter to analyze cardiac
function, from videos. It contains several filters to identify the heart region,
to reduce video noise and to calculate heart rates. RESULTS: The proposed method
was evaluated with 32 zebrafish larval cardiac videos that were recording at
three-day post-fertilization. The heart rate measured by the proposed method was
comparable to that determined by manual counting. The experimental results show
that the proposed method does not lose accuracy while largely reducing the labor
cost and uncertainty of manual counting. CONCLUSIONS: With the proposed method,
researchers do not have to manually select a region of interest before analyzing
videos. Moreover, filters designed to reduce video noise can alleviate background
fluctuations during the video recording stage (e.g. shifting), which makes
recorders generate usable videos easily and therefore reduce manual efforts while
recording.

An automatic method to calculate heart rate from zebrafish larval cardiac videos.

zebrafish is a tool to compute zebrafish heart rate using larval cardiac videos. The zebrafish algorithm includes filters to pinpoint the heart region and reduce noise.

zebrafish

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