Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice

Mathew L. Rynes, Daniel A. Surinach, Samantha Linn, Michael Laroque, Vijay Rajendran, Judith Dominguez, Orestes Hadjistamoulou, Zahra S. Navabi, Leila Ghanbari, Gregory W. Johnson, Mojtaba Nazari, Majid H. Mohajerani, Suhasa B. Kodandaramaiah

Research output: Contribution to journalArticlepeer-review

32 Scopus citations


The advent of genetically encoded calcium indicators, along with surgical preparations such as thinned skulls or refractive-index-matched skulls, has enabled mesoscale cortical activity imaging in head-fixed mice. However, neural activity during unrestrained behavior substantially differs from neural activity in head-fixed animals. For whole-cortex imaging in freely behaving mice, we present the ‘mini-mScope’, a widefield, miniaturized, head-mounted fluorescence microscope that is compatible with transparent polymer skull preparations. With a field of view of 8 × 10 mm2 and weighing less than 4 g, the mini-mScope can image most of the mouse dorsal cortex with resolutions ranging from 39 to 56 µm. We used the mini-mScope to record mesoscale calcium activity across the dorsal cortex during sensory-evoked stimuli, open field behaviors, social interactions and transitions from wakefulness to sleep.

Original languageEnglish (US)
Pages (from-to)417-425
Number of pages9
JournalNature Methods
Issue number4
StatePublished - Apr 1 2021

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© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.


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