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

• DOI: 10.1371/journal.pone.0300628
• Publication Date: 2024-03-22T17:21:17Z
• Authors: Enrico Lanza; Valeria Lucente; Martina Nicoletti; Silvia Schwartz; Ilaria F. Cavallo; Davide Caprini; Christopher W. Co...; Mashel Fatema A. ...; Julia M. Miller; Noelle D. L’Etoile; Viola Folli
• Keywords: Interface (matter); Tracking (education)

In the emerging field of whole-brain imaging at single-cell resolution, which represents one new frontiers to investigate link between brain activity and behavior, nematode Caenorhabditis elegans offers most characterized models for systems neuroscience. Whole-brain recordings consist 3D time series volumes that need be processed obtain neuronal traces. Current solutions this task are either computationally demanding or limited specific acquisition setups. Here, we propose See Elegans, a direct programming algorithm combines different techniques automatic neuron segmentation tracking without RFP channel, compare it with other available algorithms. While outperforming them in cases, our solution novel method guide identification subset head neurons based on position activity. The built-in interface allows user follow manually curate each processing steps. Elegans is thus simple-to-use aimed speeding up post-processing volumetric calcium while maintaining high level accuracy low computational demands. (Contact: [e-mail] ).