Automated, high-throughput measurement of size and growth curves of small organisms in well plates

Spheroid counter (Cell3imager) measured diameter against microscope measured length.
Spheroid counter (Cell3imager) measured diameter against microscope measured length.

Organism size and growth curves are important biological characteristics. Current methods to measure organism size, and in particular growth curves, are often resource intensive because they involve many manual steps. Here we demonstrate a method for automated, high-throughput measurements of size and growth in individual aquatic invertebrates kept in microtiter well-plates. We use a spheroid counter (Cell3iMager, cc-5000) to automatically measure size of seven different freshwater invertebrate species. Further, we generated calibration curves (linear regressions, all p < 0.0001, r2 >=0.9 for Ceriodaphnoa dubia, Asellus aquaticus, Daphnia magna, Daphnia pulex; r2 >=0.8 for Hyalella azteca, Chironomus spec. larvae and Culex spec. larvae) to convert size measured on the spheroid counter to traditional, microscope based, length measurements, which follow the longest orientation of the body. Finally, we demonstrate semi-automated measurement of growth curves of individual daphnids (C. dubia and D. magna) over time and find that the quality of individual growth curves varies, partly due to methodological reasons. Nevertheless, this novel method could be adopted to other species and represents a step change in experimental throughput for measuring organisms’ shape, size and growth curves. It is also a significant qualitative improvement by enabling high-throughput assessment of inter-individual variation of growth.

(open access link)


EFSA scientific opinion on TKTD models

The EFSA scientific opinion on TKTD modelling has been published! Read here...


New Book: Modelling survival under chemical stress

Survival is a relevant endpoint for many questions related to the effects of chemicals in the environment. Making sense of mortality, as a process over time, requires mechanism-based models, known as toxicokinetic-toxicodynamic (TKTD) models. All published TKTD models for survival can now be viewed as members of an over-arching framework: GUTS.


Click on the book cover or here to view the e-book.



1 Introduction

2 Description of GUTS

3 Mathematical treatment

4 Case study: dieldrin in guppies

5 Case study: propiconazole in amphipods

6 Use cases

7 Ring test

8 Model evaluation

9 Outlook




Physiological modes of action across species and toxicants: the key to predictive ecotoxicology

Ecotoxicologists need tools to identify those combinations of man-made chemicals and organisms most likely to cause problems. In other words: which of the millions of species are at risk from pollution? And which of the tens of thousands of chemicals contribute most to the risk? We identified our poor knowledge on physiological modes of action (how a chemical affects the energy allocation in an organism), and how they vary across species and toxicants, as a major knowledge gap. We also find that the key to predictive ecotoxicology is the systematic, rigorous characterization of physiological modes of action because that will enable more powerful in vitro to in vivo toxicity extrapolation and in silico ecotoxicology. In the near future, we expect a step change in our ability to study physiological modes of action by improved, and partially automated, experimental methods. Once we have populated the matrix of species and toxicants with sufficient physiological mode of action data we can look for patterns, and from those patterns infer general rules, theory and models. (open access, link to paper at ESPI)