Megapixel camera arrays for high-resolution animal tracking in multiwell plates

Abstract

Tracking small laboratory animals such as flies, fish, and worms is used for phenotyping in neuroscience, genetics, disease modelling, and drug discovery. Current imaging systems are limited either in spatial resolution or throughput. A system capable of imaging a large number of animals with sufficient resolution to estimate their pose would enable a new class of experiments where detailed behavioural differences are quantified but at a scale where hundreds of treatments can be tested simultaneously. Here we report a new imaging system consisting of an array of six 12-megapixel cameras that can simultaneously record from all the wells of a 96-well plate with a resolution of 80 pixels/mm at 25 frames per second. We show that this resolution is sufficient to estimate the pose of nematode worms including head identification and to extract high-dimensional phenotypic fingerprints. We illustrate the potential application of the system in three domains with a study of behavioural variability across wild isolates, experiments on the escape response and sensitisation of worms to repeated blue light stimulation, and the utility of this stimulus for phenotyping disease models. Because the system is compatible with standard multiwell plates, it makes computational ethological approaches accessible in existing high-throughput pipelines and greatly increases the scale of possible phenotypic screening experiments in C. elegans.

Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy and periventricular calcifications

“…Videos were acquired and processed following methods previously described in detail 25 . Briefly, videos were acquired in a room with a nominal temperature of 20°C at 25 frames per second and a resolution of 12.4 µm px -1 .…”

Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy, and periventricular calcifications

“…Videos were acquired and processed following methods previously described in detail. 36 Briefly, videos were acquired in a room with a nominal temperature of 20 C at 25 frames per second and a resolution of 12.4 mm px À1 . Three videos were taken sequentially: a 5-min pre-stimulus video; a 6-min blue light recording with three 10-s blue light pulses starting at 60, 160, and 260 s; and a 5-min post-stimulus recording.…”

Precise Quantification of Behavioral Individuality From 80 Million Decisions Across 183,000 Flies

“…Increasing behavioral assay throughput via automation is an effective way to attain the sample sizes needed to study variability. This can be achieved through miniaturization and parallelization of imaging platforms in a lab context ( Kain et al, 2012 ; Churgin et al, 2017 ; Pantoja et al, 2017 ; Stern et al, 2017 ; Barlow et al, 2021 ). While the up-scaling of experiments is easiest with small, lab-adapted animals, such approaches do work with species beyond the common genetic models ( Crall et al, 2016 , 2018 ; Bierbach et al, 2017 ; Ulrich et al, 2018 ).…”