Automated staging of zebrafish embryos using machine learning

Abstract

The zebrafish (Danio rerio), is an important biomedical model organism used in many disciplines, including development, disease modeling and toxicology, to better understand vertebrate biology. The phenomenon of developmental delay in zebrafish embryos has been widely reported as part of a mutant or treatment-induced phenotype, and accurate characterization of such delays is imperative. Despite this, the only way at present to identify and quantify these delays is through manual observation, which is both time-consuming and subjective. Machine learning approaches in biology are rapidly becoming part of the toolkit used by researchers to address complex questions. In this work, we introduce a machine learning-based classifier that has been trained to detect temporal developmental differences across groups of zebrafish embryos. Our classifier is capable of rapidly analyzing thousands of images, allowing comparisons of developmental temporal rates to be assessed across and between experimental groups of embryos. Finally, as our classifier uses images obtained from a standard live-imaging widefield microscope and camera set-up, we envisage it will be readily accessible to the zebrafish community, and prove to be a valuable resource.

Automated staging of zebrafish embryos with deep learning

“…Each image in the training dataset is annotated with its associated hpf. However, it is known that Datasets A and B are the same as those used in a previously published study (Jones et al, 2022). All data are available to download from the BioImage Archive (Hartley et al, 2022).…”

“…All images used for training and testing are summarised in Table 1. The details of acquisition for the images comprising datasets "A" and "B" can be found in the study of Jones et al (2022). Datasets "C" and 'D" were acquired as follows.…”

“…We recently published a machine learning-based method for the staging of zebrafish embryos (Jones et al, 2022). Although this method successfully discriminated between different populations of zebrafish developing at different rates, the developmental profiles it produced were distinctly non-linear.…”