Gigapixel imaging with a novel multi-camera array microscope
- Duke University, United States
- Ramona Optics Inc, United States
Abstract
The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from structures that approach the cellular scale to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies with a field of view over hundreds of square centimeters at an optical resolution of 18 µm. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. Further, the MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Overall, by removing the bottlenecks imposed by single-camera image acquisition systems, the MCAM provides a powerful platform for investigating detailed biological features and behavioral processes of small model organisms across a wide range of spatial scales.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files;Source Data files and associated analysis code have been provided on https://gitlab.oit.duke.edu/ean26/gigapixelimaging.To view associated MCAM videos with flexible zooming capabilities see https://gigazoom.rc.duke.edu/team/Gigapixel%20behavioral%20and%20neural%20activity%20imaging%20with%20a%20novel%20multi-camera%20array%20microscope/Owl.Other MCAM source data can be viewed at https://gigazoom.rc.duke.edu/Raw MCAM video data as well as other relevant manuscript data for all experiments is publicly available at https://doi.org/10.7924/r4nv9kp8v.
Article and author information
Author details
Funding
Alfred P. Sloan Foundation (Sloan Foundation)
- Eva A Naumann
Office of Research Infrastructure Programs, National Institutes of Health (SBIR R44OD024879)
- Eric Thomson
- Mark Harfouche
- Sunanda Sharma
- Timothy W Dunn
- Eva A Naumann
National Cancer Institute (SBIR R44CA250877)
- Mark Harfouche
- Sunanda Sharma
- Jaehee Park
National Science Foundation (NSF 2036439)
- Mark Harfouche
- Sunanda Sharma
- Jaehee Park
National Institute of Biomedical Imaging and Bioengineering (SBIR R43EB030979-01)
- Mark Harfouche
- Sunanda Sharma
- Jaehee Park
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All experiments followed the US Public Health Service Policy on Humane Care and Use of Laboratory Animals, under the protocol A083-21-04 approved by the Institutional Animal Care and Use Committee (IACUC) of Duke University School of Medicine. All experiments on zebrafish were performed according to these standards and every effort was made to minimize suffering.
Copyright
© 2022, Thomson et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 3,651
- views
-
- 526
- downloads
-
- 19
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Gigapixel imaging with a novel multi-camera array microscope
eLife 11:e74988.
https://doi.org/10.7554/eLife.74988
Further reading
-
- Neuroscience
Memory consolidation during sleep depends on the interregional coupling of slow waves, spindles, and sharp wave-ripples (SWRs), across the cortex, thalamus, and hippocampus. The reuniens nucleus of the thalamus, linking the medial prefrontal cortex (mPFC) and the hippocampus, may facilitate interregional coupling during sleep. To test this hypothesis, we used intracellular, extracellular unit and local field potential recordings in anesthetized and head restrained non-anesthetized cats as well as computational modelling. Electrical stimulation of the reuniens evoked both antidromic and orthodromic intracellular mPFC responses, consistent with bidirectional functional connectivity between mPFC, reuniens and hippocampus in anesthetized state. The major finding obtained from behaving animals is that at least during NREM sleep hippocampo-reuniens-mPFC form a functional loop. SWRs facilitate the triggering of thalamic spindles, which later reach neocortex. In return, transition to mPFC UP states increase the probability of hippocampal SWRs and later modulate spindle amplitude. During REM sleep hippocampal theta activity provides periodic locking of reuniens neuronal firing and strong crosscorrelation at LFP level, but the values of reuniens-mPFC crosscorrelation was relatively low and theta power at mPFC was low. The neural mass model of this network demonstrates that the strength of bidirectional hippocampo-thalamic connections determines the coupling of oscillations, suggesting a mechanistic link between synaptic weights and the propensity for interregional synchrony. Our results demonstrate the presence of functional connectivity in hippocampo-thalamo-cortical network, but the efficacy of this connectivity is modulated by behavioral state.
-
- Neuroscience
Outcomes can vary even when choices are repeated. Such ambiguity necessitates adjusting how much to learn from each outcome by tracking its variability. The medial prefrontal cortex (mPFC) has been reported to signal the expected outcome and its discrepancy from the actual outcome (prediction error), two variables essential for controlling the learning rate. However, the source of signals that shape these coding properties remains unknown. Here, we investigated the contribution of cholinergic projections from the basal forebrain because they carry precisely timed signals about outcomes. One-photon calcium imaging revealed that as mice learned different probabilities of threat occurrence on two paths, some mPFC cells responded to threats on one of the paths, while other cells gained responses to threat omission. These threat- and omission-evoked responses were scaled to the unexpectedness of outcomes, some exhibiting a reversal in response direction when encountering surprising threats as opposed to surprising omissions. This selectivity for signed prediction errors was enhanced by optogenetic stimulation of local cholinergic terminals during threats. The enhanced threat-evoked cholinergic signals also made mice erroneously abandon the correct choice after a single threat that violated expectations, thereby decoupling their path choice from the history of threat occurrence on each path. Thus, acetylcholine modulates the encoding of surprising outcomes in the mPFC to control how much they dictate future decisions.
