Based on maximum of the Ripley’s function it computes analytically the p-value and its log.Moving from 2D to 3D improves how your ideas and concepts are shown and communicated. SODA performs a non-parametric analysis of Ripley’s function (statistical thresholding) and is more robust than parametric analysis. Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics. – Non-parametric Ripley’s analysis (SODA) (see Lagache, T., Grassart, A., Dallongeville, S., Faklaris, O., Sauvonnet, N., Dufour, A., … & Olivo-Marin, J.
The quality of the fit can be checked ( Plot K function graph to check the fit box)
spots 2 and Mean coloc distancein the output section Ripley’s analysis (parametric). These two fitting parameters appear in % of coloc.
#Non rigid alignment artec studio free#
Here, we compute the Ripley’s K function ( Step and Maximal distance for the analysis are free parameters) and fit it (avec zero-mean and unit-variance normalization) with the expected mean curve obtained when p% of detections 2 are colocalized around detections 1, at mean distance mu. Statistical analysis of molecule colocalization in bioimaging. – Parametric analysis (fit) of the Ripley’s K function (see Lagache T, Sauvonnet N, Danglot L, Olivo-Marin JC. p-value and its log are computed analytically using binomial probabilities. – Distance analysis (centers of mass 1 inside masks 2): It counts the % of detections 1 whose center of mass (position) is inside a detection 2 mask. These methods also use 2 sequences and detections sets from spot detector plugin. WARNING: input ROIs should have their Z and T position set to 0 otherwise it won’t work !ġ- “Distance between objects”-based methods. These methods are also implemented as a block: ColocalizationStudio_correlation For overlap analysis (Manders&Overlap), we use Monte-Carlo randomizations of detections’masks are used (number of MC simulations is a free parameter (10 by default)). For Pearson correlation coefficient, we compute a closed formula based on pixel scrambling and Central Limit theorem. These methods are based either on the quantification of Pearson and cross-correlation (ICCS) between fluoresecent images or between the overlap of segmented objects (detections) through Manders, or Overlap (% of segmented objects 1 that overlap more than T% with objects 2, T is a free parameter (50% by default)) analysisĭetections for overlap analysis are output of spot detector plugin. (be sure to check the “Export to Swimming-pool” box in the “Output” menu)įor each coefficient (except ICCS), a p-value and its log are provided. This plugin is decomposed into two main method classes:
Before using it, you can find here an introduction to colocalization methods. This plugin contains most of the existing colocalization methods. Lagache, T., Grassart, A., Dallongeville, S., Faklaris, O., Sauvonnet, N., Dufour, A., … & Olivo-Marin, J. SODA (object-based, non-parametric Ripley K function analysis) is described in Lagache T, Sauvonnet N, Danglot L, Olivo-Marin JC. Review of colocalization methods: SODA analysis: DocumentationĬorrelation & Overlap methods, and Parametric analysis (fit) of Ripley K function are described in