Generating semi-synthetic validation benchmarks for embryomics

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 benc...

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Bibliographic Details
Main Authors: Stegmaier, Johannes, Arz, Julian, Schott, Benjamin, Otte, Jens C., Kobitski, Andrei, Nienhaus, G. Ulrich, Strahle, Uwe, Sanders, Peter, Mikut, Ralf
Format: Conference Proceeding
Language:English
Subjects:
Algorithm design and analysis
Algorithms
Benchmark testing
Benchmarks
Cellular
Computer simulation
Dark current
Developmental Biology
Embryo
Embryomics
Embryos
Fluorescence
Image Analysis
Manuals
Microscopy
Three dimensional
Tracking
Validation Benchmarks
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Summary: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.
ISSN:1945-8452
DOI:10.1109/ISBI.2016.7493359