CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging

Kano, Masanobu; Wang, Yuteng; Srinivasan, Sakthivel; Chérasse, Yoan; Naoi, Toshie; Sugaya, Yuki; Sakurai, Takeshi; Sakaguchi, Masanori

doi:10.1101/2023.05.19.540935

2023

DOI: 10.1101/2023.05.19.540935

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CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging

Masanobu Kano

Yuteng Wang

Sakthivel Srinivasan

et al.

Abstract: Neuron-tracking algorithms exhibit suboptimal performance in calcium imaging when the same neurons are not consistently detected, as unmatched features hinder inter-session alignment. CaliAli addresses this issue by employing an alignment-before-extraction strategy that incorporates vasculature information to improve the detectability of weak signals and maximize the number of trackable neurons. By excelling in neural remapping and high spatial overlap scenarios, CaliAli paves the way toward further understand… Show more

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2024

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Cited by 2 publications

References 17 publications

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T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals

Wang,

Vergara,

Hasegawa

et al. 2024

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A miniaturized microscope (i.e., miniscope) enables the imaging of neuronal activity using calcium sensors while simultaneously manipulating that activity using opsins in freely moving animals. However, many miniscopes use light-emitting diodes with broadband emission, leading to unintentional opsin stimulation by light intended solely for calcium sensor activation (a phenomenon referred to as "biological crosstalk"). To address this issue, we previously developed a miniscope including a port for chosen light sources, such as lasers, by restructuring the open-source UCLA Miniscope v3. However, targeting the same neuronal soma for both excitable opsin stimulation and calcium sensor imaging remained a challenge. Here, we integrated features from the UCLA Miniscope v4 into our new T-scope V4 miniscope. In optogenetic tagging experiments, we demonstrated that a 445-nm blue laser can be used to image neuronal activity with the calcium sensor GCaMP6s without inadvertently stimulating the ChrimsonR opsin, allowing for simultaneous neuronal activity imaging and manipulation in freely moving mice. Thus, the T-scope V4 can serve as a powerful tool for probing causal relationships between neuronal activity and its function in living animals.

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T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals

Wang,

Vergara,

Hasegawa

et al. 2024

Preprint

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Chemotagging: a chemogenetic approach for identifying cell types within vivocalcium imaging

Ko,

Bacon,

Zaki

et al. 2024

Preprint

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The ability to monitor the activity of specific cell types in vivo is critical for understanding the complex interplay between various neuronal populations driving freely moving behavior. Existing methods, such as optogenetic tagging (i.e., Optotagging), have proven useful for identifying cell types in in vivo electrophysiological recordings during freely moving behavior. However, electrophysiological recordings are limited in their capacity to track the same neuronal populations across long periods of time (days to weeks). Single-photon miniscope imaging offers the advantage of tracking the same cells across weeks to months; however, it is difficult to distinguish different cell types within the recorded population. Here, we present "chemotagging," a technique that allows for the identification of specific cell types in in vivo calcium imaging recordings. This protocol offers a method for tagging cell types with chemogenetic tools like Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), while simultaneously recording calcium activity from a pan-neuronal population with calcium indicators. We highlight the key advantages and limitations of chemotagging and its potential implications for neuroscience research.

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CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging

Cited by 2 publications

References 17 publications

T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals

T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals

Chemotagging: a chemogenetic approach for identifying cell types within vivocalcium imaging

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