A multi-animal tracker for studying complex behaviors

Background

Animals exhibit astonishingly complex behaviors. Studying the subtle features of these behaviors requires quantitative, high-throughput, and accurate systems that can cope with the often rich perplexing data.

Results

Here, we present a Multi-Animal Tracker (MAT) that provides a user-friendly, end-to-end solution for imaging, tracking, and analyzing complex behaviors of multiple animals simultaneously. At the core of the tracker is a machine learning algorithm that provides immense flexibility to image various animals (e.g., worms, flies, zebrafish, etc.) under different experimental setups and conditions. Focusing on C. elegans worms, we demonstrate the vast advantages of using this MAT in studying complex behaviors. Beginning with chemotaxis, we show that approximately 100 animals can be tracked simultaneously, providing rich behavioral data. Interestingly, we reveal that worms’ directional changes are biased, rather than random – a strategy that significantly enhances chemotaxis performance. Next, we show that worms can integrate environmental information and that directional changes mediate the enhanced chemotaxis towards richer environments. Finally, offering high-throughput and accurate tracking, we show that the system is highly suitable for longitudinal studies of aging- and proteotoxicity-associated locomotion deficits, enabling large-scale drug and genetic screens.

Conclusions

Together, our tracker provides a powerful and simple system to study complex behaviors in a quantitative, high-throughput, and accurate manner.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0363-9) contains supplementary material, which is available to authorized users.

Uses of Human MR and PET Imaging in Research of Neurodegenerative Brain Diseases

In the past decades, many neuroimaging studies have aimed to improve the scientific understanding of human neurodegenerative diseases using MRI and PET. This article is designed to provide an overview of the major classes of brain imaging and how/why they are used in this line of research. It is intended as a primer for individuals who are relatively unfamiliar with the methods of neuroimaging research to gain a better understanding of the vocabulary and overall methodologies. It is not intended to describe or review any research findings for any disease or biology, but rather to broadly describe the imaging methodologies that are used in conducting this neurodegeneration research. We will also review challenges and strategies for analyzing neuroimaging data across multiple sites and studies, i.e., harmonization and standardization of imaging data for multi-site and meta-analyses.

Measurement of Rice Grain Dimensions and Chalkiness, and Rice Grain Elongation Using Image Analysis

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Quantification of Thrips Damage Using Ilastik and ImageJ Fiji

Quantification of insect damage is an essential measurement for identifying resistance in plants. In screening for host plant resistance against thrips, the total damaged leaf area is used as a criterion to determine resistance levels. Here we present an objective novel method for analyzing thrips damage on leaf disc using the freely available software programs Ilastik and ImageJ. The protocol was developed in order to screen over 40 Capsicum lines for resistance against Frankliniella occidentalis (Western Flower Thrips) and Thrips tabaci (Onion thrips).

Can liming change root anatomy, biomass allocation and trace element distribution among plant parts of Salix × smithiana in trace element-polluted soils?

Willows (Salix spp.) are considered to be effective for the phytoremediation of trace elements from contaminated soils, but their efficiency is limited in heavily polluted soils because of poor growth. Liming can be a desirable measure to decrease the plant availability of elements, resulting in improved plant development. Notably, large root area and maximum soil penetration are basic parameters that improve the efficiency of phytoremediation. The impact of soil chemical properties on willow root anatomy and the distribution of trace elements below-ground have rarely been studied. The effect of liming on root parameters, biomass allocation and trace element distribution in non-harvestable (coarse roots, fine roots, stumps) and harvestable plant parts (twigs and leaves) of Salix × smithiana was assessed at the end of a 4-year pot experiment with two trace element-polluted soils that differed in terms of soil pH. Stump biomass predominated in weakly acidic soil. In neutral soil, the majority of biomass was located in fine roots and stumps; the difference from other plant parts was minor. Trace elements were the most concentrated in fine roots. Translocation to above-ground biomass increased as follows: Pb < As < Zn~Cd. In contrast to Cd and Zn, great differences in As and Pb mobility in plants were recorded after measurements of individual below-ground biomass (stumps < coarse roots < fine roots). Lime application decreased the concentrations of mobile Cd and Zn and related levels in plants, improved biomass production and root parameters and increased the removal of all trace elements in weakly acidic soil. None or minimum differences in the monitored parameters were recorded for dolomite treatments in both soils. The dose and source of liming had crucial effects on root anatomy. Growing willows in limed trace element-polluted soils is a suitable measure for combination of two remediation strategies, i.e. phytoextraction of Cd and Zn and assisted phytostabilization of As and Pb.

Analysis of centrosomal area actin reorganization and centrosome polarization upon lymphocyte activation at the immunological synapse

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