Designing a large field-of-view two-photon microscope using optical invariant analysis

AbstractBackgroundMotion correction is a challenging pre-processing problem that arises early in the analysis pipeline of calcium imaging data sequences. The motion artifacts in two-photon microscopy recordings can be non-rigid, arising from the finite time of raster scanning and non-uniform deformations of the brain medium.New methodWe introduce an algorithm for fast Non-Rigid Motion Correction (NoRMCorre) based on template matching. NoRMCorre operates by splitting the field of view into overlapping spatial patches that are registered at a sub-pixel resolution for rigid translation against a continuously updated template. The estimated alignments are subsequently up-sampled to create a smooth motion field for each frame that can efficiently approximate non-rigid motion in a piecewise-rigid manner.Existing methodsExisting approaches either do not scale well in terms of computational performance or are targeted to motion artifacts arising from low speed scanning, whereas modern datasets with large field of view are more prone to non-rigid brain deformation issues.ResultsNoRMCorre can be run in an online mode resulting in comparable to or even faster than real time motion registration on streaming data. We evaluate the performance of the proposed method with simple yet intuitive metrics and compare against other non-rigid registration methods on two-photon calcium imaging datasets. Open source Matlab and Python code is also made available.ConclusionsThe proposed method and code provide valuable support to the community for solving large scale image registration problems in calcium imaging, especially when non-rigid deformations are present in the acquired data.

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A spatio-temporally compensated acousto-optic scanner for two-photon microscopy providing large field of view

Optics Express ◽

10.1364/oe.16.010066 ◽

2008 ◽

Vol 16 (14) ◽

pp. 10066 ◽

Cited By ~ 32

Author(s):

Y. Kremer ◽

J.-F. Léger ◽

R. Lapole ◽

N. Honnorat ◽

Y. Candela ◽

...

Keyword(s):

Field Of View ◽

Large Field ◽

Two Photon Microscopy ◽

Two Photon

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Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry

10.1101/2020.09.20.305508 ◽

2020 ◽

Cited By ~ 1

Author(s):

Che-Hang Yu ◽

Jeffrey N. Stirman ◽

Yiyi Yu ◽

Riichiro Hira ◽

Spencer L. Smith

Keyword(s):

Adaptive Optics ◽

Calcium Imaging ◽

High Speed ◽

Optical Design ◽

Neural Circuitry ◽

Brain Regions ◽

Field Of View ◽

Large Field ◽

Two Photon ◽

Subcellular Resolution

AbstractImaging the activity of neurons that are widely distributed across brain regions deep in scattering tissue at high speed remains challenging. Here, we introduce an open-source system with Dual Independent Enhanced Scan Engines for Large Field-of-view Two-Photon imaging (Diesel2p). Combining novel optical design, adaptive optics, and temporal multiplexing, the system offers subcellular resolution over a large field-of-view (∼ 25 mm2) with independent scan engines. We demonstrate the flexibility and various use cases of this system for calcium imaging of neurons in the living brain.

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