Calcium image analysis in the moving gut.

BACKGROUND: The neural control of gastrointestinal muscle relies on circuit activity whose underlying motifs remain limited by small-sample calcium imaging recordings confounded by motion artifact, paralytics, and muscle dissections. We present a sequence of resources to register images from moving preparations and identify out-of-focus events in widefield fluorescent microscopy. METHODS: Our algorithm uses piecewise rigid registration with pathfinding to correct movements associated with smooth muscle contractions. We developed methods to identify loss-of-focus events and to simulate calcium activity to evaluate registration. KEY RESULTS: By combining our methods with principal component analysis, we found populations of neurons exhibit distinct activity patterns in response to distinct stimuli consistent with hypothesized roles. The image analysis pipeline makes deeper insights possible by capturing concurrently calcium dynamics from more neurons in larger fields of view. We provide access to the source code for our algorithms and make experimental and technical recommendations to increase data quality in calcium imaging experiments. CONCLUSIONS: These methods make feasible large population, robust calcium imaging recordings and permit more sophisticated network analyses and insights into neural activity patterns in the gut.

Rational engineering of ratiometric calcium sensors with bright green and red fluorescent proteins.

Ratiometric genetically encoded calcium indicators (GECIs) record neural activity with high brightness while mitigating motion-induced artifacts. Recently developed ratiometric GECIs primarily employ cyan and yellow-fluorescent fluorescence resonance energy transfer pairs, and thus fall short in some applications that require deep tissue penetration and resistance to photobleaching. We engineered a set of green-red ratiometric calcium sensors that fused two fluorescent proteins and calcium sensing domain within an alternate configuration. The best performing elements of this palette of sensors, Twitch-GR and Twitch-NR, inherited the superior photophysical properties of their constituent fluorescent proteins. These properties enabled our sensors to outperform existing ratiometric calcium sensors in brightness and photobleaching metrics. In turn, the shot-noise limited signal fidelity of our sensors when reporting action potentials in cultured neurons and in the awake behaving mice was higher than the fidelity of existing sensors. Our sensor enabled a regime of imaging that simultaneously captured neural structure and function down to the deep layers of the mouse cortex.

Decontaminate Traces From Fluorescence Calcium Imaging Videos Using Targeted Non-negative Matrix Factorization.

Fluorescence microscopy and genetically encoded calcium indicators help understand brain function by recording large-scale in vivo videos in assorted animal models. Extracting the fluorescent transients that represent active periods of individual neurons is a key step when analyzing imaging videos. Non-specific calcium sources and background adjacent to segmented neurons contaminate the neurons' temporal traces with false transients. We developed and characterized a novel method, temporal unmixing of calcium traces (TUnCaT), to quickly and accurately unmix the calcium signals of neighboring neurons and background. Our algorithm used background subtraction to remove the false transients caused by background fluctuations, and then applied targeted non-negative matrix factorization to remove the false transients caused by neighboring calcium sources. TUnCaT was more accurate than existing algorithms when processing multiple experimental and simulated datasets. TUnCaT's speed was faster than or comparable to existing algorithms.

Hybrid light-sheet and light-field microscope for high resolution and large volume neuroimaging.

Large scale simultaneous recording of fast patterns of neural activity remains challenging. Volumetric imaging modalities such as scanning-beam light-sheet microscopy (LSM) and wide-field light-field microscopy (WFLFM) fall short of the goal due to their complex calibration procedure, low spatial resolution, or high-photobleaching. Here, we demonstrate a hybrid light-sheet light-field microscopy (LSLFM) modality that yields high spatial resolution with simplified alignment of the imaging plane and the excitation plane. This new modality combines the selective excitation of light-sheet illumination with volumetric light-field imaging. This modality overcomes the current limitations of the scanning-beam LSM and WFLFM implementations. Compared with LSM, LSLFM captures volumetric data at a frame rate 50× lower than the rate of LSM and requires no dynamic calibration. Compared with WFLFM, LSLFM produces moderate improvements in spatial resolutions, 10 times improvement in the contrast when imaging fluorescent beads, and 3.2× the signal-to-noise ratio in the detection of neural activity when imaging live zebrafish expressing a genetically encoded calcium sensor.