Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale
Journal article, 2016

The capacity to map traits over large cohorts of individuals—phenomics—lags far behind the explosive development in genomics. For microbes, the estimation of growth is the key phenotype because of its link to fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved growth phenotypes at an unprecedented scale. Advancements were achieved through the introduction of transmissive scanning hardware and software technology, frequent acquisition of exact colony population size measurements, extraction of population growth rates from growth curves, and removal of spatial bias by reference-surface normalization. Our prototype arrangement automatically records and analyzes close to 100,000 growth curves in parallel. We demonstrate the power of the approach by extending and nuancing the known salt-defense biology in baker’s yeast. The introduced framework represents a major advance in microbial phenomics by providing high-quality data for extensive cohorts of individuals and generating well-populated and standardized phenomics databases


open source

high throughput



micro biology



Martin Zackrisson

University of Gothenburg

Johan Hallin

Université Nice Sophia Antipolis (UNS)

Lars-Göran Ottosson

University of Gothenburg

Peter Dahl

University of Gothenburg

Esteban Fernandez-Parada

University of Gothenburg

Erik Ländström

University of Gothenburg

Luciano Fernandez-Ricaud

University of Gothenburg

Petra Kaferle

Jozef Stefan Institute

Andreas Skyman

Chalmers, Earth and Space Sciences, Plasma Physics and Fusion Energy

Simon Stenberg

University of Gothenburg

Stig Omholt

Norwegian University of Science and Technology (NTNU)

Uros Petrovic

Jozef Stefan Institute

Jonas Warringer

University of Gothenburg

Anders Blomberg

University of Gothenburg

G3: Genes, Genomes, Genetics

21601836 (eISSN)

Vol. 6 9 3003-3014

Subject Categories

Biochemistry and Molecular Biology

Bioengineering Equipment



Other Industrial Biotechnology


Basic sciences



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