ArticleNature protocols2021
Chronic, cortex-wide imaging of specific cell populations during behavior.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Ultrafast venous and sagittal sinus constrictions in the brain driven by abdominal pressure.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Large field of view fluorescence imaging of microfluidic devices with a tandem-lens macroscope.Lab on a chip · 2026Article
- CortexCAM: A Camera Array Microscope for Cortex-Wide Cellular Imaging in Freely Locomoting Mice.Research square · 2026Article
- STIMscope: centimeter-scale all-optical imaging and patterned optogenetic manipulation at single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- Intrinsic space-time couplings governing multi-scale cortical dynamics.bioRxiv : the preprint server for biology · 2026Article
- NeuroPupil: A generalization-first framework for scalable and biologically informative cross-species pupillometry.bioRxiv : the preprint server for biology · 2026Article
- Choosing a skull clearing technique for chronic mesoscopic optical imaging in awake mice.Neurophotonics · 2026Article
- Syngap1 Synchronizes Relative Neuronal Maturation Across Cortical Areas to Organize Distributed Functional Networks.bioRxiv : the preprint server for biology · 2026Article
- Rapid dynamics of dorsal raphe serotonin neurons regulate the strength of visual attention.Nature communications · 2026Article
- Corticothalamic communication for action coordination in a skilled motor behavior.Nature neuroscience · 2026Article
- Neural barcoding representing cortical spatiotemporal dynamics based on continuous-time Markov chains.Cell reports methods · 2026Article
- Multiparametric imaging of spatio-temporal cAMP signaling, transmembrane potential, and intracellular calcium in the intact heart.iScience · 2026Article
- Cortex-Wide Cellular Imaging in Freely Locomoting Mice Using Cortex Camera Array Microscope (CortexCAM).bioRxiv : the preprint server for biology · 2026Article
- Multi-scale imaging and recording of in-vivo neural activity.BMB reports · 2026Review
- Simultaneous thermal and large field-of-view two-photon imaging enables optimization of signal-to-noise.Neurophotonics · 2026Article
- Large field of view fluorescence imaging of microfluidic devices with a tandem-lens macroscopebioRxiv : the preprint server for biology · 2025Article
- Establishing a continuum of cell types in the visual cortex.bioRxiv : the preprint server for biology · 2025Article
- Spontaneous movements and their relationship to neural activity fluctuate with latent engagement states.Neuron · 2025Article
- Early and widespread cerebellar engagement during hippocampal seizures and interictal discharges.Neurobiology of disease · 2025Article
- Purkinje Cell Spatial Correlation Dynamics Are Key to Cerebellar Cortical Contributions to Behavior.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes such as attention, decision-making and action selection. However, techniques that allow cellular resolution measurements are expensive and require a high degree of technical expertise, which limits their broad use. Wide-field imaging of genetically encoded indicators is a high-throughput, cost-effective and flexible approach to measure activity of specific cell populations with high temporal resolution and a cortex-wide field of view. Here we outline our protocol for assembling a wide-field macroscope setup, performing surgery to prepare the intact skull and imaging neural activity chronically in behaving, transgenic mice. Further, we highlight a processing pipeline that leverages novel, cloud-based methods to analyze large-scale imaging datasets. The protocol targets laboratories that are seeking to build macroscopes, optimize surgical procedures for long-term chronic imaging and/or analyze cortex-wide neuronal recordings. The entire protocol, including steps for assembly and calibration of the macroscope, surgical preparation, imaging and data analysis, requires a total of 8 h. It is designed to be accessible to laboratories with limited expertise in imaging methods or interest in high-throughput imaging during behavior.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.