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Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging


To understand neural circuit mechanisms underlying behavior, it is crucial to observe the dynamics of neuronal structure and function in different regions of the brain. Since current noninvasive imaging technologies allow cellular-resolution imaging of neurons only within ~1 mm below the cortical surface, the majority of mouse brain tissue remains inaccessible. While miniature optical imaging probes allow access to deep brain regions, cellular-resolution imaging is typically restricted to a small tissue volume. To increase the tissue access volume, we developed a clear optically matched panoramic access channel technique (COMPACT). With probe dimensions comparable to those of common gradient-index lenses, COMPACT enables a two to three orders of magnitude greater tissue access volume. We demonstrated the capabilities of COMPACT by multiregional calcium imaging in mice during sleep. We believe that large-volume in vivo imaging with COMPACT will be valuable to a variety of deep tissue imaging applications.

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Fig. 1: System design of COMPACT.
Fig. 2: In vivo imaging of neuronal structure at different depths in the Thy1-eGFP mouse brain.
Fig. 3: In vivo calcium imaging in the brain of a head-fixed awake mouse.
Fig. 4: Neurons in different regions showed distinct activity associated with sleep.

Data availability

The imaging datasets generated during and/or analyzed during the current study are available at and Source data for Figs. 3 and 4 and Extended Data Fig. 7 are provided with this paper.

Code availability

The code employed in the measurement and data analysis is available at


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This work was funded by the NIH (grant nos. U01NS094341, U01NS107689, U01NS118302 to M.C.) and Purdue University. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. M.C. thanks S. Sternson (HHMI Janelia research campus) and J. Isaacson (UCSD) for valuable comments and discussion, and thanks the Howard Hughes Medical Institute for scientific instruments.

Author information




M.C. invented COMPACT and designed and implemented the imaging system. M.C. and W.-B.G. supervised the research. W.-B.G. designed the biology experiment. B.W., C.W. and Z.C. collaborated on the experiment, data analysis and figure preparation. B.L. assisted the EEG/EMG and sleep studies. All authors contributed to the writing of the manuscript.

Corresponding author

Correspondence to Meng Cui.

Ethics declarations

Competing interests

In March 2020, Purdue University filed a utility patent for the COMPACT-based deep brain neurophotonic interface (inventor Meng Cui; U.S. Application No 16/833,550), which covered the concept, design and implementation of COMPACT.

Additional information

Peer review information Nina Vogt was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Procedure for imaging probe alignment.

(a) Optical setup for probe alignment. (b) Images from camera 1 and 2. (c) Capillary alignment. (d) Top view of the capillary.

Extended Data Fig. 2 High-resolution compound probe for two-photon COMPACT imaging.

(a) Compound lens configuration. (b) Two-photon imaging of 0.5 μm fluorescence beads. (c, d) The imaging point spread function for imaging 100 and 400 μm outside the capillary, respectively. (e) Two-photon imaging of Thy1-eGFP mouse brain with an imaging depth of 1.8 mm. The maximum working distance reached 450 μm. (f) Neuronal structures at the indicated working distances.

Extended Data Fig. 3 Comparison of COMPACT imaging and dissected tissue imaging in Thy1-eGFP mouse brain.

(a, b) Image comparison for the bottom of the imaging volume (COMPACT probe at 0 degree). (c, d) Comparison for the region at which the COMPACT probe was at 24 degree. (e, f) Comparison for the region at which the COMPACT probe was at 52 degree.

Extended Data Fig. 4 Surgical procedure for capillary implantation.

(a) Design of the head-bar for head fixed animal imaging. (b) Illustration of the surgical procedures during capillary implantation.

Extended Data Fig. 5 Docking method for the imaging probe.

(a, b) Illustration of the docking approach for holding the imaging probe in place. (c) A quick-release probe holder for fine adjustment of probe orientation and depth. We employed this probe docking method for the calcium imaging of awake mice, which is shown in Supplementary Video 5.

Extended Data Fig. 6 Repeated probe insertion and imaging.

Cell locations before and after reloading the animal to the imaging system. The probe insertion repeatability can be reproduced in all experiments.

Extended Data Fig. 7 COMPACT-based calcium imaging with simultaneous electromyography (EMG) and electroencephalography (EEG) recording.

(a–c) Imaging locations for ROI 1 and 2. (d, e) Representative images showing calcium activity of neurons during awake and asleep states in ROI 1 and 2, respectively. The imaging experiments were repeated independently on 5 mice with similar results. (f, g) The EMG, EEG, ΔF/F0 of each cell and their average in ROI 1 and 2, respectively. The awake and asleep states are labeled on top, which was based on the EMG signal levels.

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–5 and Table 1.

Reporting Summary

Supplementary Video 1

Design of the two-photon COMPACT imaging system. The optical configuration of the two-photon imaging system and the operation of whole-depth panoramic two-photon imaging.

Supplementary Video 2

Two-photon structural imaging of Thy1-eGFP mouse brain. The acquisition of the image volume shown in Supplementary Fig. 1b.

Supplementary Video 3

Comparison of COMPACT imaging and dissected tissue imaging in Thy1-eGFP mouse brain. The acquisition of the images shown in Extended Data Fig. 2.

Supplementary Video 4

Two-photon calcium imaging of awake mouse brain. The acquisition of the image volume shown in Fig. 3.

Supplementary Video 5

Two-photon calcium imaging of awake mouse brain using the probe docking method.

Supplementary Video 6

Longitudinal multiregional calcium imaging of neuronal activity associated with pupil size.

Source data

Source Data Fig. 3

Calcium activity source data.

Source Data Fig. 4

Calcium activity source data, pupil size source data, statistical source data.

Source Data Extended Data Fig. 7

EMG/EEG, calcium activity source data.

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Wei, B., Wang, C., Cheng, Z. et al. Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging. Nat Methods 18, 959–964 (2021).

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