A versatile toolbox for semi-automatic cell-by-cell object-based colocalization analysis

Differential fluorescence labeling and multi-fluorescence imaging followed by colocalization analysis is commonly used to investigate cellular heterogeneity in situ. This is particularly important when investigating the biology of tissues with diverse cell types. Object-based colocalization analysis...

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Bibliographic Details
Published inScientific reports Vol. 10; no. 1; p. 19027
Main Authors Lunde, Anders, Glover, Joel C.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 04.11.2020
Nature Publishing Group
Subjects
631/114/1564
631/337
Accuracy
Algorithms
Automation
Automation - methods
Central nervous system
Fluorescence
Heterogeneity
Humanities and Social Sciences
Image Processing, Computer-Assisted - methods
Labeling
multidisciplinary
Nervous system
Noise
Science
Science (multidisciplinary)
Segmentation
Visualization
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Summary:Differential fluorescence labeling and multi-fluorescence imaging followed by colocalization analysis is commonly used to investigate cellular heterogeneity in situ. This is particularly important when investigating the biology of tissues with diverse cell types. Object-based colocalization analysis (OBCA) tools can employ automatic approaches, which are sensitive to errors in cell segmentation, or manual approaches, which can be impractical and tedious. Here, we present a novel set of tools for OBCA using a semi-automatic approach, consisting of two ImageJ plugins, a Microsoft Excel macro, and a MATLAB script. One ImageJ plugin enables customizable processing of multichannel 3D images for enhanced visualization of features relevant to OBCA, and another enables semi-automatic colocalization quantification. The Excel macro and the MATLAB script enable data organization and 3D visualization of object data across image series. The tools are well suited for experiments involving complex and large image data sets, and can be used in combination or as individual components, allowing flexible, efficient and accurate OBCA. Here we demonstrate their utility in immunohistochemical analyses of the developing central nervous system, which is characterized by complexity in the number and distribution of cell types, and by high cell packing densities, which can both create challenging situations for OBCA.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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HSØ/2013022
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-020-75835-7