Abstract
BackgroundAnalyzing spatial distributions of objects in images is a fundamental task in many biological studies. The relative arrangement of a set of objects with respect to another set of objects contains information about potential interactions between the two sets of objects. If they do not “feel” each other’s presence, their spatial distributions are expected to be independent of one another. Spatial correlations in their distributions are indicative of interactions and can be modeled by an effective interaction potential acting between the points of the two sets. This can be used to generalize co-localization analysis to spatial interaction analysis. However, no user-friendly software for this type of analysis was available so far.ResultsWe present an ImageJ/Fiji plugin that implements the complete workflow of spatial pattern and interaction analysis for spot-like objects. The plugin detects objects in images, infers the interaction potential that is most likely to explain the observed pattern, and provides statistical tests for whether an inferred interaction is significant given the number of objects detected in the images and the size of the space within which they can distribute. We benchmark and demonstrate the present software using examples from confocal and PALM single-molecule microscopy.ConclusionsThe present software greatly simplifies spatial interaction analysis for point patterns, and makes it available to the large user community of ImageJ and Fiji. The presented showcases illustrate the usage of the software.
Highlights
Analyzing spatial distributions of objects in images is a fundamental task in many biological studies
We show here the application of the plugin to two real-world cases: interactions between viruses and endosomes in HER-911 cells as inferred from fluorescence confocal microscopy images, and clathrin–G-protein-coupled receptors (GPCRs) interactions as inferred from Photo-Activation Localization Microscopy (PALM) super-resolution data in HeLa cells
Application to virus–endosome interaction from confocal images We apply the plugin to analyze the interactions between human adenoviruses of serotype 2 (Ad2), stained with ATTO-647, and Rab5-EGFP-stained endosomes in HER911 cells
Summary
We present an ImageJ/Fiji plugin that implements the complete workflow of spatial pattern and interaction analysis for spot-like objects. The plugin detects objects in images, infers the interaction potential that is most likely to explain the observed pattern, and provides statistical tests for whether an inferred interaction is significant given the number of objects detected in the images and the size of the space within which they can distribute. We benchmark and demonstrate the present software using examples from confocal and PALM single-molecule microscopy
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