Experiment/xie 2026 mouse dorsal cortex
From Miniscope
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Mouse dorsal cortex layer 2/3 imaging with MIMAS during open-field exploration
Sparse layer 2/3 GCaMP6f imaging across most of the dorsal cortex through a large trapezoid cranial window, with a lightweight microlens-array scope worn by freely moving mice in a 30 min open-field session.
Extracted from full textTranscribed by a curator from the published methods section. Values not stated in the paper are marked as not reported rather than inferred.
Animal
Species
Mouse
Strain
C57BL/6J
Transgenic line
Rasgrf2-2A-dCre (JAX 022864) x Ai148 (JAX 030328)
Sex
Both
Age at surgery
8-16 weeks
Animals
3 mice (2 of them in the position-modulation analysis)
Indicator
Indicator
GCaMP6f
Reports
Calcium
Delivery
Transgenic
Expression time
Trimethoprim (50 mg/kg, intraperitoneal) given about 1 week before surgery to induce expression
Optical access
Method
Cranial window
Lens
Trapezoid glass coverslip: 7 mm top base, 9 mm bottom base, 7.2-7.4 mm tall, about 0.15 mm thick
Implant to baseplating
After the window cleared, typically about 2 weeks after surgery; the focal plane was first found with the mouse head-fixed
Imaging
Condition
Freely behaving
Frame rate
9.3 fps typical (18 fps with 2 x 2 sensor binning)
Sessions
One 30 min open-field session per mouse
Behavior
Free exploration of a 50 x 50 x 40 cm open field
Analysis
SUPPORT denoising, CaImAn (MATLAB) per subfield, custom duplicate-cell removal, OASIS, DeepLabCut, CEBRA
Cell yield
3,652 neurons from 3 mice after quality control and duplicate removal; 2,904 neurons in the 2 mice used for position modulation
What was hard about this preparation
The authors note that sparse labeling made per-subfield extraction and duplicate removal tractable, and that denser labeling will need better segmentation and cross-subfield matching. Reconstruction is offline and depends on accurate subfield registration. Neurons in overlapping subfields are detected more than once and must be removed after stitching. It is a one-photon surface-imaging scope, so depth is limited and out-of-plane fluorescence may matter in scattering or densely labeled tissue.
Who to ask
Experimenter
Changliang Guo, Liangyi Chen, Wenhao Liu, Qiang Fu
Institution
Peking University; Harbin Institute of Technology; Changchun Institute of Optics, Fine Mechanics and Physics
Notes
Field of view is about 4 x 4.5 mm. The scope weighs 2.31 g and imaged 16 of its 20 lenslets, limited by the sensor area. Wearing it did not change distance traveled, time in the center, or mean or maximum speed over 30 min in three mice. A headpost was cemented over the cerebellum. The detachable LED ring and its holder double as the baseplate. Anatomical assignment used Allen CCFv3. Build files and documentation are at https://doi.org/10.5281/zenodo.21787351. The paper also images FITC-dextran vasculature in head-fixed mice under isoflurane; that is a different preparation and is not entered here.