Generating Semi-Synthetic Validation Benchmarks for Embryomics

TL;DR

This paper introduces a semi-synthetic method for creating realistic 3D+t benchmarks in embryomics, combining real embryo dynamics with simulated imaging to improve validation of image analysis algorithms.

Contribution

A novel semi-synthetic benchmark generation approach that integrates real cellular dynamics with simulated imaging artifacts for embryomics.

Findings

Successfully simulated zebrafish embryo development with thousands of cells

Generated realistic benchmarks incorporating cellular movement and imaging distortions

Enhanced validation capabilities for embryo image analysis algorithms

Abstract

Systematic validation is an essential part of algorithm development. The enormous dataset sizes and the complexity observed in many recent time-resolved 3D fluorescence microscopy imaging experiments, however, prohibit a comprehensive manual ground truth generation. Moreover, existing simulated benchmarks in this field are often too simple or too specialized to sufficiently validate the observed image analysis problems. We present a new semi-synthetic approach to generate realistic 3D+t benchmarks that combines challenging cellular movement dynamics of real embryos with simulated fluorescent nuclei and artificial image distortions including various parametrizable options like cell numbers, acquisition deficiencies or multiview simulations. We successfully applied the approach to simulate the development of a zebrafish embryo with thousands of cells over 14 hours of its early existence.