Resources

This protocol runs the SODA analysis for 2 colors images (a third channel is used to define the ROI). Results and ROIs s [..]

Created on: 28 Feb 2018
No reviews
Modified: 12 Nov 2018

This protocol runs SODA analysis on 3 colours fluorescence images, export SODA results and ROI statistics for single spo [..]

Created on: 28 Feb 2018
No reviews
Modified: 28 Feb 2018

This protocol runs the SODA analysis on 2D STORM images. It imports localizations from files, run SODA, export results a [..]

Created on: 24 Feb 2018
No reviews
Modified: 24 Feb 2018

This block draw color crosses from arrays of 2D localizations. It is particularly useful for data mapping and visualization of STORM images.

Created on: 24 Feb 2018
No reviews
Modified: 24 Feb 2018

This protocol runs the SODA analysis from 3D STORM images. Inputs are (excel) files with (x,y,z) localizations, and outp [..]

Created on: 23 Feb 2018
No reviews
Modified: 23 Feb 2018

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Created on: 23 Feb 2018
No reviews
Modified: 14 Aug 2019

This block implements the DBSCAN algorithm in 2D and 3D.

Created on: 16 Feb 2018
No reviews
Modified: 22 Feb 2018

This protocol’s block draws 3D spheres with VTK from a list of cartesian coordinates (x,y,z). It is used by SODA-STORM [..]

Created on: 16 Feb 2018
No reviews
Modified: 16 Feb 2018

This plugin aims at simulating 2D time-lapse Total Internal Reflection Fluorescence (TIRF) microscope images of endocytosis.

Created on: 09 Feb 2018
No reviews
Modified: 09 Feb 2018

This protocol extracts the statistical percentage and distance of colocalization between 2 color molecule spots

Created on: 30 Nov 2015
No reviews
Modified: 30 Nov 2015

This protocol computes the Pearson and Manders coefficients between 2 spotty images (the masks of spots that are needed [..]

Created on: 30 Nov 2015
No reviews
Modified: 30 Nov 2015

This protocol, designed for the microbiology course at Institut Pasteur, allows to extract cell masks, and actin and lis [..]

Created on: 20 Oct 2015
No reviews
Modified: 20 Oct 2015

Tracking plugin specifically designed for tracking of endocytosis/exocytosis in TIRF microscopy

Created on: 18 Sep 2015
No reviews
Modified: 26 Apr 2017

This plugin computes the Manders coefficients between ROIs in 2 sequences (Intensity and surface coefficients). A p valu [..]

Created on: 01 Sep 2014
1 review
Modified: 23 Jan 2015

Create two synthetic sequences with given numbers of spots and colocalization properties (percentage, distance mean and standard deviation)

Created on: 01 Sep 2014
No reviews
Modified: 12 Jun 2015

This plugin contains most of existing colocalization methods in 2D and 3D fluorescence microscopy images: Pearson and Ma [..]

Created on: 29 Aug 2014
3 reviews
Modified: 19 Jun 2020

This block can be used to filter ROIs as function of their circularity 2*pi*area/(perimeter^2). The output ROIs are the [..]

Created on: 24 Jan 2014
No reviews
Modified: 24 Jan 2014

Input = Rois and Detections (viewed as ROIs) Output= Rois that contain at least one Detection and the Detections that are in at least one of the Rois

Created on: 10 Dec 2013
No reviews
Modified: 11 Jun 2015

This block plugin compute the intersection between the union of Rois 1 and the union of Rois 2: (union Rois 1) inter (union Rois 2)

Created on: 10 Dec 2013
No reviews
Modified: 10 Dec 2013

This protocol counts the number of cells with signal aggregates in the neighborhood of cell nuclei (Golgi aparitus...) [..]

Created on: 10 Dec 2013
No reviews
Modified: 24 Jan 2014

This protocol counts the number of stained cells in a population of cells. It requires at least 2 color channels: one co [..]

Created on: 10 Dec 2013
No reviews
Modified: 17 Jan 2014

This plugin uses the Ripley’s K function to analyze robustly the spatial organization of molecules.

Created on: 31 Oct 2013
1 review
Modified: 30 Mar 2020

This plugins allows debleaching of time sequences of fluorescence images.

Created on: 29 Nov 2012
1 review
Modified: 29 Nov 2012