MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis

BMC Bioinformatics

Arun Shivanandan¹  Aleksandra Radenovic¹  Ivo F Sbalzarini² 

[1] Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland

[2] Previously: MOSAIC Group, Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland

关键词: Image analysis;    Fiji;    ImageJ;    PALM;    Interaction analysis;    Co-localization analysis;    Microscopy;    Spatial pattern analysis;   

Others  :  1087689
DOI  :  10.1186/1471-2105-14-349

 received in 2013-05-29, accepted in 2013-11-08,  发布年份 2013

【 摘 要 】

Background

Analyzing 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.

Results

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.

Conclusions

The 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.

【 授权许可】

   
2013 Shivanandan et al.; licensee BioMed Central Ltd.

【 图 表 】

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