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1. An end-to-end recurrent compressed sensing method to denoise, detect and demix calcium imaging data

   https://doi.org/10.1038/s42256-024-00892-w  

   Zhang, Kangning; Tang, Sean; Zhu, Vivian; Barchini, Majd; Yang, Weijian (September 2024, Nature Machine Intelligence)

   Two-photon calcium imaging provides large-scale recordings of neuronal activities at cellular resolution. A robust, automated and high-speed pipeline to simultaneously segment the spatial footprints of neurons and extract their temporal activity traces while decontaminating them from background, noise and overlapping neurons is highly desirable to analyse calcium imaging data. Here we demonstrate DeepCaImX, an end-to-end deep learning method based on an iterative shrinkage-thresholding algorithm and a long short-term memory neural network to achieve the above goals altogether at a very high speed and without any manually tuned hyperparameter. DeepCaImX is a multi-task, multi-class and multi-label segmentation method composed of a compressed sensing-inspired neural network with a recurrent layer and fully connected layers. The neural network can simultaneously generate accurate neuronal footprints and extract clean neuronal activity traces from calcium imaging data. We trained the neural network with simulated datasets and benchmarked it against existing state-of-the-art methods with in vivo experimental data. DeepCaImX outperforms existing methods in the quality of segmentation and temporal trace extraction as well as processing speed. DeepCaImX is highly scalable and will benefit the analysis of mesoscale calcium imaging. 

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2. Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators

   https://doi.org/10.7554/eLife.25690  

   Chamberland, Simon; Yang, Helen H; Pan, Michael M; Evans, Stephen W; Guan, Sihui; Chavarha, Mariya; Yang, Ying; Salesse, Charleen; Wu, Haodi; Wu, Joseph C; et al (July 2017, eLife)

   Monitoring voltage dynamics in defined neurons deep in the brain is critical for unraveling the function of neuronal circuits but is challenging due to the limited performance of existing tools. In particular, while genetically encoded voltage indicators have shown promise for optical detection of voltage transients, many indicators exhibit low sensitivity when imaged under two-photon illumination. Previous studies thus fell short of visualizing voltage dynamics in individual neurons in single trials. Here, we report ASAP2s, a novel voltage indicator with improved sensitivity. By imaging ASAP2s using random-access multi-photon microscopy, we demonstrate robust single-trial detection of action potentials in organotypic slice cultures. We also show that ASAP2s enables two-photon imaging of graded potentials in organotypic slice cultures and in Drosophila. These results demonstrate that the combination of ASAP2s and fast two-photon imaging methods enables detection of neural electrical activity with subcellular spatial resolution and millisecond-timescale precision. 

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3. Relative phase of membrane potential theta oscillations between individual hippocampal neurons code space

   https://doi.org/10.1101/2025.11.14.688496  

   Athif, Mohamed; Malmberg, Samantha; Mount, Rebecca; Patel, Kush; Wang, Yangyang; Shaw, Dana; Ravasio, Cara; Xiao, Sheng; Rillosi, Enrico; Tseng, Hua-an; et al (November 2025, bioRxiv)

   ABSTRACT The timing of spikes dictates a neuron’s impact on downstream circuits and behavior, and spike timing is determined by the membrane potential (Vm). However, due to technical challenges, it has been impossible to analyze the relative timing of Vm dynamics between neurons during behavior. Using large scale membrane voltage imaging, we simultaneously recorded Vm from many individual hippocampal neurons in animals engaged in a virtual spatial task. We found that relative phase of Vm theta oscillations across neurons exhibit gradual or discrete shifts depending on spatial position. This finding extends beyond previous studies showing Vm dynamics in single neurons or spiking activity in multiple neurons, revealing previously unknown evidence for consistent coding of space by spike-independent relative phase of Vm theta dynamics between neurons. 

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4. Compressive Fourier-Domain Intensity Coupling (C-FOCUS) enables near-millimeter deep imaging in the intact mouse brain in vivo

   https://doi.org/10.21203/rs.3.rs-7104566/v1  

   Xue, Yi; He, Renzhi; Li, Yucheng; Urbina, Brianna; Wan, Jiandi (July 2025, Research Square)

   Abstract Two-photon microscopy is a powerful tool for in vivo imaging, but its imaging depth is typically limited to a few hundred microns due to tissue scattering, even with existing scattering correction techniques. Moreover, most active scattering correction methods are restricted to small regions by the optical memory effect. Here, we introduce compressive Fourier-domain intensity coupling for scattering correction (C-FOCUS), an active scattering correction approach that integrates Fourier-domain intensity modulation with compressive sensing for two-photon microscopy. Using C-FOCUS, we demonstrate high-resolution imaging of YFP labeled neurons and FITC-labeled blood vessels at depths exceeding 900 µm in the intact mouse brain in vivo. Furthermore, we achieve transcranial imaging of YFP-labeled dendritic structures through the intact adult mouse skull. C-FOCUS enables high-contrast fluorescence imaging at depths previously inaccessible using two-photon microscopy with 1035 nm excitation, enhancing fluorescence intensity by over 20-fold compared to uncorrected imaging. C-FOCUS provides a broadly applicable strategy for rapid, deep-tissue optical imaging in vivo. 

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5. In toto imaging of early enteric nervous system development reveals that gut colonization is tied to proliferation downstream of Ret

   https://doi.org/10.1242/dev.200668  

   Baker, Phillip A.; Ibarra-García-Padilla, Rodrigo; Venkatesh, Akshaya; Singleton, Eileen W.; Uribe, Rosa. A. (November 2022, Development)

   ABSTRACT The enteric nervous system is a vast intrinsic network of neurons and glia within the gastrointestinal tract and is largely derived from enteric neural crest cells (ENCCs) that emigrate into the gut during vertebrate embryonic development. Study of ENCC migration dynamics and their genetic regulators provides great insights into fundamentals of collective cell migration and nervous system formation, and these are pertinent subjects for study due to their relevance to the human congenital disease Hirschsprung disease (HSCR). For the first time, we performed in toto gut imaging and single-cell generation tracing of ENCC migration in wild type and a novel ret heterozygous background zebrafish (retwmr1/+) to gain insight into ENCC dynamics in vivo. We observed that retwmr1/+ zebrafish produced fewer ENCCs localized along the gut, and these ENCCs failed to reach the hindgut, resulting in HSCR-like phenotypes. Specifically, we observed a proliferation-dependent migration mechanism, where cell divisions were associated with inter-cell distances and migration speed. Lastly, we detected a premature neuronal differentiation gene expression signature in retwmr1/+ ENCCs. These results suggest that Ret signaling may regulate maintenance of a stem state in ENCCs. 

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