Generating Semi-Synthetic Validation Benchmarks for Embryomics
This addresses the problem of insufficient validation tools for algorithm developers in embryomics, though it is incremental as it builds on existing simulation methods.
The authors tackled the lack of realistic validation benchmarks for time-resolved 3D fluorescence microscopy in embryomics by developing a semi-synthetic approach that combines real embryo dynamics with simulated nuclei and distortions, successfully simulating zebrafish embryo development over 14 hours with thousands of cells.
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.