![]() Furthermore, some kidney pathological conditions, such as the glomerulocystic disease, could originate from topological defects acquired during development ( Fiorentino et al., 2020). This can be fundamental in studies of mitochondrial metabolism where a complex correlation between ER-mitochondria Ca 2+ fluxes and autophagy have been highlighted ( Missiroli et al., 2020). Similarly, in experiments where the measurement of transient concentration of Ca 2+ or metabolites is assessed, a stable staining and reliable segmentation of individual cytoplasmic organelles might be required to then apply a “2D measurement” of fluorescence intensity and organelle shape ( Supplementary Figure S1B). For instance, the counting of protein structures, such as the ProMyelocytic Leukemia Nuclear Bodies (PML NB) found involved in chromatin remodeling, telomere biology, senescence or viral infections ( Lallemand-Breitenbach and de The, 2018), is achievable by applying a “2D counting” image analysis tool to first identify cells and then determine the number of contained PML NB ( Supplementary Figure S1A). However, researchers operating microscopes have to deal with a number of experimental challenges often requiring different types of image analysis procedures. Microscopy and image analysis significantly contribute to the advancement of research in life sciences. This plugin aims to provide interactive and zero-scripting customizable workflows for cell segmentation, vesicles counting, parent-child relation between objects, signal quantification, and results presentation all included in the same open-source napari viewer, and “few clicks away”. Here we present ZELDA, a new napari plugin that easily integrates the cutting-edge solutions offered by python ecosystem, such as scikit-image for image segmentation, matplotlib for data visualization, and napari multi-dimensional image viewer for 3D rendering. While several commercial packages are available on the market, fewer are the open-source solutions able to execute a complete 3D analysis workflow. Despite the availability of numerous algorithms for the 2D and 3D segmentation, the latter still offers some challenges for the end-users, who often do not have either an extensive knowledge of the existing software or coding skills to link the output of multiple tools. Furthermore, it is increasingly appreciated that to overcome the limitations of the 2D-view-based image analysis approaches and to correctly understand and interpret biological processes, a 3D segmentation of microscopy data sets becomes imperative. ![]() 2Department of Biology and Biochemistry, University of Bath, Bath, United Kingdomīioimage analysis workflows allow the measurement of sample properties such as fluorescence intensity and polarization, cell number, and vesicles distribution, but often require the integration of multiple software tools.1Crick Advanced Light Microscopy STP, The Francis Crick Institute, London, United Kingdom.Rocco D’Antuono 1* and Giuseppina Pisignano 2 ![]()
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