Spot fluorescence and perinuclear enrichment Thibault Lagache This protocol defines two ROIs based on nuclear fluorescence (DAPI). Nuclear ROIs are first extracted using the HK-mean [..] Created on: 14 Jan 2026 No reviews Modified: 14 Jan 2026
Dynamics Classifier (TrackProcessor) Thibault Lagache This track processor split tracks into tracklets and statistically classifies each tracklet as Brownian/confined or dire [..] Created on: 20 Sep 2022 No reviews Modified: 12 Dec 2022
Tracks Colocalizer Thibault Lagache This track processor is specifically designed for 2-color imaging of endocytosis at the cell membrane. It determines the [..] Created on: 20 Jan 2022 No reviews Modified: 20 Jan 2022
Detection (with cluster un-mixing) and tracking of neurons with EMC2 Thibault Lagache This protocol 1- detects bright spots (neurons) with Wavelet spot detector 2- un-mix (i.e. detects individual spots in l [..] Created on: 02 Jul 2020 No reviews Modified: 02 Jul 2020
Laplacian of Gaussian (LoG) convolution (2D) Thibault Lagache This plugin (block) is performing the 2D convolution of a sequence with the Laplacian of Gaussian (LoG) kernel Created on: 01 Jul 2020 No reviews Modified: 03 Aug 2020
Detection and Tracking of neurons with EMC2 Thibault Lagache This protocol is designed to track neurons in calcium imaging of behaving animal. It contains a step of spot detection ( [..] Created on: 01 Jul 2020 No reviews Modified: 01 Jul 2020
Elastic motion correction and concatenation (EMC2) of tracks Thibault Lagache EMC2 plugin & block(s) is designed for closing tracking gaps in single-particle tracking. It is particularly well-su [..] Created on: 01 Jul 2020 No reviews Modified: 10 Sep 2021
Spot detection and colocalization (object) analysis Copy Thibault Lagache This protocol extract detections and performs object-based colocalization analysis with ColocalizationStudio_object bloc Created on: 17 Jan 2019 No reviews Modified: 28 Jun 2018
Spot detection and colocalization (object) analysis Thibault Lagache This protocol extract detections and performs object-based colocalization analysis with ColocalizationStudio_object bloc Created on: 28 Jun 2018 No reviews Modified: 28 Jun 2018
Spot detection and colocalization (correlation) analysis Thibault Lagache This protocol detects objects in sequences 1&2, and performs colocalization analysis (correlation & overlap) with coloca [..] Created on: 28 Jun 2018 No reviews Modified: 28 Jun 2018
SODA 2 Colours Thibault Lagache 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
SODA 3 Colours Thibault Lagache 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
SODA STORM 2D Thibault Lagache 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
Draw 2D points Thibault Lagache 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
SODA STORM 3D Thibault Lagache 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
Import localizations from files Thibault Lagache This block imports localizations (x,y,z) and nb of photons from excel files. Outputs are arrays of doubles. Created on: 23 Feb 2018 No reviews Modified: 23 Feb 2018
SODA suite Thibault Lagache 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: 27 May 2021
Sequence generator Thibault Lagache This block generate a black Icy sequence with desired dimensions. Created on: 17 Feb 2018 No reviews Modified: 17 Feb 2018
DBSCAN Thibault Lagache This block implements the DBSCAN algorithm in 2D and 3D. Created on: 16 Feb 2018 No reviews Modified: 22 Feb 2018
Draw 3D Spheres with VTK Thibault Lagache 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: 03 Apr 2023
Endocytosis Simulator Thibault Lagache 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
coloc_object.protocol Thibault Lagache 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
coloc_correlation.protocol Thibault Lagache 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
protocolTPMicrobio Thibault Lagache 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
eTrack Thibault Lagache Tracking plugin specifically designed for tracking of endocytosis/exocytosis in TIRF microscopy Created on: 18 Sep 2015 No reviews Modified: 09 Mar 2021
Manders Thibault Lagache 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
Colocalization Simulator Thibault Lagache 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
Colocalization Studio Thibault Lagache This plugin contains most of existing colocalization methods in 2D and 3D fluorescence microscopy images: Pearson and Ma [..] Created on: 29 Aug 2014 5 reviews Modified: 04 Nov 2021
Circularity filter Thibault Lagache 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
Detections in Rois Thibault Lagache 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
Multiple intersections Thibault Lagache 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
Cells with aggregates Thibault Lagache 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
Stained cells Thibault Lagache 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
Spatial Analysis Thibault Lagache 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
Anisotropy profiler Thibault Lagache This plugin measures the percentage of elongated spots in a sequence. Created on: 29 Oct 2013 No reviews Modified: 29 Oct 2013
Compaction profiler Thibault Lagache This plugin permit to measure the signal spread of a molecule with respect to the cell area. Created on: 10 Dec 2012 2 reviews Modified: 26 Nov 2020
Debleach Thibault Lagache This plugins allows debleaching of time sequences of fluorescence images. Created on: 29 Nov 2012 1 review Modified: 30 Sep 2020
