title: MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis.
abstract: 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.
authors.affiliation: MOSAIC Group, Center of Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr 108, 01307 Dresden, Germany. ivos@mpi-cbg.de.
authors.forename: Arun
authors.initials: A
authors.lastname: Shivanandan
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Radenovic
authors.forename: Ivo F
authors.initials: IF
authors.lastname: Sbalzarini
mesh_terms: D000260:Adenoviruses, Human / Q000737:chemistry / Q000378:metabolism; D000465:Algorithms; D002460:Cell Line; D011992:Endosomes / Q000737:chemistry / Q000378:metabolism / Q000821:virology; D049452:Green Fluorescent Proteins / Q000737:chemistry; D006801:Humans; D018613:Microscopy, Confocal / Q000379:methods; D057054:Molecular Imaging; D009010:Monte Carlo Method; D011336:Probability; D011897:Random Allocation; D012984:Software; D062211:Spatio-Temporal Analysis
chemical_list: C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins