ezTrack: An open-source video analysis pipeline for the investigation of animal behavior

Pennington, Zachary T.; Dong, Zhe; Bowler, Regina; Feng, Yu; Vetere, Lauren M.; Shuman, Tristan; Cai, Denise J.

doi:10.1101/592592

Cited by 18 publications

(15 citation statements)

References 14 publications

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“…From the resulting calcium transients, fast non-negative deconvolution (Zhou et al, 2018) was used for specific analyses to deconvolve the fluorescent changes of each neuron into approximations of the underlying neural activity. Animal position was tracked using ezTrack (Pennington et al, 2019).…”

Section: Calcium Video Processingmentioning

confidence: 99%

HippoBellum: Acute Cerebellar Modulation Alters Hippocampal Dynamics and Function

2020

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Here we examine what effects acute manipulation of the cerebellum, a canonically motor structure, can have on the hippocampus, a canonically cognitive structure. In male and female mice, acute perturbation of the cerebellar vermis (lobule 4/5) or simplex produced reliable and specific effects in hippocampal function at cellular, population, and behavioral levels, including evoked local field potentials, increased hippocampal cFos expression, and altered CA1 calcium event rate, amplitudes, and correlated activity. We additionally noted a selective deficit on an object location memory task, which requires objection-location pairing. We therefore combined cerebellar optogenetic stimulation and CA1 calcium imaging with an object-exploration task, and found that cerebellar stimulation reduced the representation of place fields near objects, and prevented a shift in representation to the novel location when an object was moved. Together, these results clearly demonstrate that acute modulation of the cerebellum alters hippocampal function, and further illustrates that the cerebellum can influence cognitive domains.

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Section: Calcium Video Processingmentioning

confidence: 99%

HippoBellum: Acute Cerebellar Modulation Alters Hippocampal Dynamics and Function

2020

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“…Robust tracking was previously demonstrated using DLC [14] and other open source tracking software (e.g. ezTrack) [41] , thus we established DLC tracking in arenas that are compatible with the commercial systems we routinely use in our lab. We labeled standardized points of interest when tracking the mouse in each test (Figure 1a).…”

Section: Resultsmentioning

confidence: 95%

Deep learning based behavioral analysis enables high precision rodent tracking and is capable of outperforming commercial solutions

Sturman

Ziegler

Schläppi

et al. 2020

Preprint

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To study brain function, preclinical research relies heavily on animal monitoring and the subsequent analyses of behavior. Commercial platforms have enabled semi high-throughput behavioral analyses by providing accurate tracking of animals, yet they often struggle with the analysis of ethologically relevant behaviors and lack the flexibility to adapt to variable testing environments. In the last couple of years, substantial advances in deep learning and machine vision have given researchers the ability to take behavioral analysis entirely into their own hands. Here, we directly compare the performance of commercially available platforms (Ethovision XT14, Noldus; TSE Multi Conditioning System, TSE Systems) to cross-verified human annotation. To this end, we provide a set of videos -carefully annotated by several human raters -of three widely used behavioral tests (open field, elevated plus maze, forced swim test). Using these data, we show that by combining deep learning-based motion tracking (DeepLabCut) with simple post-analysis, we can track animals in a range of classic behavioral tests at similar or even greater accuracy than commercial behavioral solutions. In addition, we integrate the tracking data from DeepLabCut with post analysis supervised machine learning approaches. This combination allows us to score ethologically relevant behaviors with similar accuracy to humans, the current gold standard, thus outperforming commercial solutions. Moreover, the resulting machine learning approach eliminates variation both within and between human annotators. In summary, our approach helps to improve the quality and accuracy of behavioral data, outperforming commercial systems at a fraction of the cost.

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“…This is because even when the mice were freezing, the movement in the optogenetic cable was calculated by the software as movement. Hence for optogenetic behavioral experiments, we analyzed freezing using ezTrack software (Pennington, Dong et al 2019), which enables removal of this cable artifact. In brief, videos were cropped to reduce the influence of optogenetic cables in the upper portion of the field of view.…”

Section: Data Are Presented As Mean Percentages (+/− Sem)mentioning

confidence: 99%

A Basomedial Amygdala to Intercalated Cells Microcircuit Expressing PACAP and Its Receptor PAC1 Regulates Contextual Fear

et al. 2021

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Author Contributions Section: AKR designed the studies, ran experiments, and wrote the manuscript. JCO performed electrophysiological experiments. ZP helped with optogenetic behavioral experiment analysis. FM ran VGLUT2 RNAscope experiments. SG and JT helped with optogenetic experiments. JC, NE and NK helped with behavioral experiments. WZH provided the Adcyap1-2A-Cre mice. RLN made the HSV viruses used in the intersectional viral approach. JW made and provided the PAC1 loxP/loxP and the Adcyap1-EGFP mice. BSK helped with all aspects of electrophysiological experiments and supervised JCO. The electrophysiology experiments were designed by AKR and MSF. MSF supervised all the studies and helped design the experiments and manuscript preparation.

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ezTrack: An open-source video analysis pipeline for the investigation of animal behavior

Cited by 18 publications

References 14 publications

HippoBellum: Acute Cerebellar Modulation Alters Hippocampal Dynamics and Function

HippoBellum: Acute Cerebellar Modulation Alters Hippocampal Dynamics and Function

Deep learning based behavioral analysis enables high precision rodent tracking and is capable of outperforming commercial solutions

A Basomedial Amygdala to Intercalated Cells Microcircuit Expressing PACAP and Its Receptor PAC1 Regulates Contextual Fear

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