Tracking activity of neurons across weeks from 1-photon calcium imaging

Wärnberg, EmilKTH,Beräkningsvetenskap och beräkningsteknik (CST),Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden (författare)

QC 20231101
One-photon calcium imaging using head-mounted miniaturized endoscopes ("miniscopes") is a powerful method for imaging neuron activity of genetically-labeled neurons with single-cellresolution from awake and freely moving animals. A major challenge in analysis of imagingdata is the recording of single neurons over multiple days. To improve speed and accuracy,we created a software package for calcium extraction with a highly optimized GPU-basedimplementation of the Constrained Non-negative Matrix Factorization (CNMF) algorithmwith OASIS deconvolution of the traces. Additionally, we introduce negentropy as a robust statistical measure to rapidly initialize spatial footprints as well as to automatically find the best regularization and time constant of the OASIS deconvolution. We found that our implementation is 50x-100x faster compared to a state-of-the-art calcium processing tool. The significant speed advantage enables processing of a large number of calcium videos from separate recording days as a single concatenated video, making it feasible to follow individual cells across multiple days in a consistent manner. We demonstrate how our approach can capture the neural dynamics across more than two weeks of daily recordings with 1-photon miniscope of Oprm1-Cre+ striatal projection neurons as mice develop a task strategy in a maze.

Skara, VasilikiDepartment of Neuroscience, Karolinska Institutet, Stockholm, Sweden (författare)
Mantas, IoannisDepartment of Neuroscience, Karolinska Institutet, Stockholm, Sweden (författare)
Meletis, KonstantinosDepartment of Neuroscience, Karolinska Institutet, Stockholm, Sweden (författare)
KTHBeräkningsvetenskap och beräkningsteknik (CST) (creator_code:org_t)

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MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Neurovetenskaper

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