kCSD-python, reliable current source density estimation with quality control
kCSD-python, reliable current source density estimation with quality control
Abstract Interpretation of the extracellular recordings can be difficult due to the long range of electric field but can be facilitated by estimating the density of current sources (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method, and introduce several new techniques to facilitate CSD analysis of experimental data and interpretation of the results. We investigate the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter notebook tutorial to facilitate uptake by the community.
Chintaluri Chaitanya、Czerwi¨?ski Micha?、W¨?jcik Daniel K.、J?drzejewska-Szmek Joanna、?redniawa W?adys?aw、Dzik Jakub M.、Bejtka Marta
Laboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences||Institute of Science and Technology AustriaLaboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of SciencesLaboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of SciencesLaboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of SciencesLaboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences||University of Warsaw, Faculty of Biology, Department of ZoologyLaboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of SciencesLaboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences
生物物理学计算技术、计算机技术生物科学研究方法、生物科学研究技术
Chintaluri Chaitanya,Czerwi¨?ski Micha?,W¨?jcik Daniel K.,J?drzejewska-Szmek Joanna,?redniawa W?adys?aw,Dzik Jakub M.,Bejtka Marta.kCSD-python, reliable current source density estimation with quality control[EB/OL].(2025-03-28)[2025-05-10].https://www.biorxiv.org/content/10.1101/708511.点此复制
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