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Fig. 1 | BMC Bioinformatics

Fig. 1

From: PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

Fig. 1

Use cases showing examples of PartSeg analysis performed on 3D confocal images of rat hippocampal neurons and mouse neuroblastoma cell line. A. Distribution of chromosome 1 and 16 territories (CTs) in a neuronal nucleus. A.a Confocal picture of a single, segmented nucleus with CT 1 (upper panel, green) and CT 16 (lower panel, red) visualised by FISH. A.b Quantification of volume and surface of CT 1 (segmented with MSO algorithm) and CT 16 (segmented with manual threshold). A.c Radial distribution of CTs 1 and 16 volume within a neuronal nucleus. Concentric spheres depicted for chromosome 1 as A, B and C have an equal radius. A.d Perinuclear distribution of CT 1 and 16 . CT volume located within 1500 nm from the nucleus boundary (depicted for chromosome 16) was measured for each chromosome. B Distribution of Npas4 gene within a neuronal nucleus and chromosome 1 CT. B.a Confocal picture of a single, segmented nucleus with chromosome 1 (depicted in red) and Npas4 gene (depicted in green) visualised by FISH. B.b Segmentation of Npas4 gene and its localization in a neuronal nucleus. B.c Segmentation of Npas 4 gene and chromosome 1 CT, graphs show Npas4 localisation relative to CT. C Neuronal nucleus and chromatin analysis. C.a DNA staining of a neuronal nucleus. C.b Segmentation of neuronal nucleus based on DNA staining. Quantification of nuclear diameter and volume. C.c Quantification of average DNA volume based on segmentation using Otsu automated threshold. C.d Quantification of chromocenters based on segmentation using Rényi Entropy automated threshold, graphs show chromocenters number, relative volume, and percentage of chromocenters volume localised within 800 nm from the nuclear border. D Quantification of PML bodies. D.a Confocal picture of a single, segmented nucleus of a mouse neuroblastoma cell line with PML bodies depicted in red. D.b Segmentation of PML bodies and quantification of their number, diameter, and volume

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