Detection and colocalization of autophagic and lysosomal vesicles in muscle fibers celine Malleval Loisel This protocol enables batch detection, statistics, and colocalization of autophagic vesicles labeled with CYTO-ID (green [..] Created on: 03 Mar 2026 No reviews Modified: 03 Mar 2026
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
ROI intensity XLS export over frames and slices Stephane Dallongeville ROI intensity evolution XLS export (all frames and slices) Created on: 16 Jun 2023 No reviews Modified: 16 Jun 2023
Separate ROIs with watershed Stephane Dallongeville Simple protocols to separate a set of ROIs using Watershed process. The input ROIs are replaced by the separation result. Created on: 17 Jan 2023 No reviews Modified: 17 Jan 2023
Flatten image in RGB (screenshot) and save it in JPG Stephane Dallongeville This is a simple protocol demonstrating the screenshot block which take an input sequence and build a new ARGB sequence [..] Created on: 13 Jan 2023 No reviews Modified: 13 Jan 2023
Amyloid clusters colocalisation on synapses Pauline Bouvet The protocol was created to calculate the percentage of synapses that contains clusters of a peptide. It first defines s [..] Created on: 07 Jun 2022 No reviews Modified: 07 Jun 2022
XLS export of spots intensity over time Stephane Dallongeville Export ROIs intensity evolution over time in XLS Created on: 25 Apr 2022 No reviews Modified: 25 Apr 2022
Convert frame – time to channel example Stephane Dallongeville Simple protocol to demonstrate how to convert a time Sequence to channel Sequence (Time –> Channel) Created on: 06 Apr 2022 No reviews Modified: 06 Apr 2022
Leaf area counter Giordano Basili Luciani this protocols allow to calculate internal leaf area. first of all, the destination excel file need to be create in orde [..] Created on: 01 Dec 2021 No reviews Modified: 01 Dec 2021
Cells detection and tracking with Active Contour Stephane Dallongeville Cells detection and tracking with Active Contour. RAW tracks export + tracks motion export in XLS format. Created on: 15 Sep 2021 No reviews Modified: 15 Sep 2021
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
Batch spots detections and statistics Marion Louveaux Batch spots detections and statistics Created on: 01 Jul 2020 No reviews Modified: 24 Sep 2020
Spots detection and colocalisation analysis with SODA Marion Louveaux Spots detection and colocalisation analysis with SODA Created on: 01 Jul 2020 No reviews Modified: 01 Jul 2020
Nuclei segmentation from maximum intensity projections Marion Louveaux Project 3D stacks in 2D (maximum intensity projection along Z axis) and segments nuclei stained with Hoechst. [..] Created on: 01 Jul 2020 No reviews Modified: 24 Sep 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
Easy SODA – 2 colors – 1 image IcyLyd This protocol allows you to use easily ICY SODA plugin to analyse colocalization and/or indirect association between 2 c [..] Created on: 28 Jun 2020 No reviews Modified: 27 May 2021
Easy Cell shape with HK-Means IcyLyd This protocol allows you to segment Cell shape thanks to the HK-Means method. It will create an overlay of the segmented [..] Created on: 22 Jun 2020 No reviews Modified: 18 Mar 2021
Rainbow Spot detector scale finder IcyLyd This protocol helps you to find the right scale sensitivity when using the spot detector plugin, to get the most adapt [..] Created on: 22 Jun 2020 No reviews Modified: 22 Jun 2020
P3 – Characterize the PSF from beads in 3D Corinne Lorenzo Jordi Andilla Corinne Lorenzo Jordi Andilla Characterizes the PSF in 3D in the entire volume of a light-sheet image containing fluorescent beads. Related protocols: [..] Created on: 18 Jun 2020 No reviews Modified: 27 Jan 2021
P2 – SNR and contrast measurements Corinne Lorenzo Jordi Andilla Corinne Lorenzo Jordi Andilla Measures the SNR, Contrast Index (CI), Normalized Contrast Index (NCI) and Contrasted Imaging Volume (CIV) on the extrac [..] Created on: 18 Jun 2020 No reviews Modified: 27 Jan 2021
P1 – Detect tissue mimics and crop 3D sub-volume Jordi Andilla Corinne Lorenzo Jordi Andilla Corinne Lorenzo Detects tissue mimics imaged with a light-sheet microscope and crops 3D sub-volume. Related protocols: P2 – SNR and co [..] Created on: 18 Jun 2020 No reviews Modified: 27 Jan 2021
Substructure Analyzer Isabelle Behm-Ansmant The Substructure Analyzer workflow allows automatic analysis of fluorescent signals in cellular compartments and measu [..] Created on: 06 Jun 2020 No reviews Modified: 18 Jun 2020
DeltaT Andrew McCall Creates a new image sequence of size n-1 from the active sequence that shows the intensity changes between each pair of [..] Created on: 28 May 2020 No reviews Modified: 28 May 2020
Cell Fluorescence Quantification Stéphane Rigaud Jessica Quintin Stéphane Rigaud Jessica Quintin Protocol for automatically segmenting cell and quantifying their area and intensity, under fluorescence binocular in bat [..] Created on: 12 Mar 2020 No reviews Modified: 12 Mar 2020
Remove ROIS touching image border Stephane Dallongeville This protocol allow to quickly remove ROIs touching the border / edge of the image. Created on: 28 May 2019 No reviews Modified: 23 Sep 2019
NewColocalizer with binary and excel output v1_batch StephO A modified version of Colocalizer with binary and excel output. The main improvement is that it processes images as batc [..] Created on: 26 Feb 2019 No reviews Modified: 26 Feb 2019
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
Big BUnwarp Registration with SURF Daniel Felipe González Obando This protocols performs big image registrations using Big BUnwarp and SURF Feature matching Needs the following plugins [..] Created on: 07 Sep 2018 No reviews Modified: 11 Jun 2020
ImageJ background subtraction Stephane Dallongeville Very basic background subtraction example using ImageJ. Created on: 01 Aug 2018 No reviews Modified: 01 Aug 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
