See Elegans: Simple-to-use, accurate, and automatic 3D detection of neural activity from densely packed neurons.

Autor: Lanza E; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy., Lucente V; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy.; D-tails s.r.l., Rome, Italy., Nicoletti M; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy.; Department of Engineering, Campus Bio-Medico University, Rome, Italy., Schwartz S; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy., Cavallo IF; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy.; D-tails s.r.l., Rome, Italy., Caprini D; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy., Connor CW; Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America., Saifuddin MFA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States of America., Miller JM; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States of America., L'Etoile ND; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, United States of America., Folli V; Center for Life Nano- and Neuro-Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy.; D-tails s.r.l., Rome, Italy.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2024 Mar 22; Vol. 19 (3), pp. e0300628. Date of Electronic Publication: 2024 Mar 22 (Print Publication: 2024).
DOI: 10.1371/journal.pone.0300628
Abstrakt: In the emerging field of whole-brain imaging at single-cell resolution, which represents one of the new frontiers to investigate the link between brain activity and behavior, the nematode Caenorhabditis elegans offers one of the most characterized models for systems neuroscience. Whole-brain recordings consist of 3D time series of volumes that need to be processed to obtain neuronal traces. Current solutions for this task are either computationally demanding or limited to specific acquisition setups. Here, we propose See Elegans, a direct programming algorithm that combines different techniques for automatic neuron segmentation and tracking without the need for the RFP channel, and we compare it with other available algorithms. While outperforming them in most cases, our solution offers a novel method to guide the identification of a subset of head neurons based on position and activity. The built-in interface allows the user to follow and manually curate each of the processing steps. See Elegans is thus a simple-to-use interface aimed at speeding up the post-processing of volumetric calcium imaging recordings while maintaining a high level of accuracy and low computational demands. (Contact: enrico.lanza@iit.it).
Competing Interests: Viola Folli is an employee and scientific advisor of D-tails s.r.l. Valeria Lucente and Ilaria Cavallo are employees of D-tails s.r.l." However, this does not alter our adherence to PLOS ONE policies on sharing data and materials.
(Copyright: © 2024 Lanza et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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