# Generating Semi-Synthetic Validation Benchmarks for Embryomics

arXiv: https://arxiv.org/abs/1604.04906 · HTML: https://mlsanity.com/paper/1604.04906/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 17 Apr 2016.

## Built on by (most cited first, 1 of 1)

- [Generative modeling of living cells with SO(3)-equivariant implicit neural representations](https://mlsanity.com/paper/2304.08960/) (2023)

## Abstract (arXiv)

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.