Fabrice de Chaumont

Track one mouse from the top-view of a cage, using an MP4 input.

Display a 2D sequence over another 2D sequence using additive blending

Detects aggregates and export results to excel file.

Helps with measuring hue values from arabidopsis plantlets on dishes. This provides a neutral tool for chlorosis scoring [..]

Interactive counter. Click on the sequence to add detection, see number of detection in ROIs directly over the sequence.

Overlay designed to be deformed to fit atlas over images

Compute a whole benchmark with all scenarios

Generates tracks for benchmark.

Display the track number on the viewer.

Enable manual annotation of TNTs

Tool for mycosis lung quantification

Block creating a file name using the one of a sequence, adding text as suffix

Layer for 3D View that displays a Bounding Box around the object.

Deprecated: Use the Xuggler Video Importer plugin instead !

This plugin should import any kind of video.

Provides track length and track displacement using the sequence scale or arbitrary unit. Also provides the number of fra [..]

Generate nice dataset animations with interpolated camera points.

Translate the tracks so that first detection is at 0,0,0 location

Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.

Displays a customizable time stamp over a 2D sequence. This book chapter proposes a video tutorial on the TimeStamp Ove [..]

Colocalizer block. See colocalization protocol.

Add a leyer on an image to display the detections

This plugin monitors your internet connection. The result image is updated every 5 seconds. 1 line per 15 minutes. A gr [..]

Reconstruct an image up to a desired scale, and do not add resulting residual.

Use this tool to create Icy’s splashscreens.

Ligand-Receptor ratio quantifier

Plots an intensity profile of a given ROI.

Can plot mean over T or/and Z too.

Substract all selected ROIs to all ROIs.

This enables scripting in Javascript directly into a block.

This enables scripting in Javascript directly into a block.

For each ROI, computes the number of pixel over a threshold. This plugin also provides the density and outputs results as an excel file.

This tool cuts existing ROIs by an angle using the graphical protractor tool. This plugin also enable pie cut or ROI.

Creates ROI rings from existing ROI
Each ROI are substracted by the first ROI of smaller surface.

Exports connected components data in XLS. Exports All, by T or by ROI

Creates a colocalization scatter plot based on 2 channels. This plugin can take 1 ROI as input, and provides the data to build the bubble excel graph.

Performs tests and write a diagnose file that can be used to understand user problem and to debug Icy.

This processor exports the tracks in an xls file (compatible with Protocols)

Wavelet Spot Detector for Blocks, to integrate in protocols.

Captures video from the webcam based on the Xuggler lib.

Tutorial on how to access single images in a video file. (Requires Icy 1.2.3)

Creates an overlay on which you can draw. This can also be used to generate specific data (for tests).

Dedicated to score tracking dataset from the ISBI tracking challenge

Record what you are doing on a sequence as a .avi file, fully compatible with Icy.

Take a screenshot of a 2D sequence with a custom magnification

Mice Profiler Video Label Maker processes tracking data to label a sequence thanks to a repertoire. This plugin is now d [..]

Mice profiler temporal analysis of data. This plugin is now directly bundled into Mice Profiler Tracker plugin [..]

Mice Profiler tracks multiple mice from a top view video.

TrackProcessor for the TrackManager plugin that allows computing several measures of tracking performance. It proceeds [..]

TrackProcessor for the TrackManager plugin that allows importing/exporting tracks. Input and output files are in the .xm [..]

Edit the workspaces with a simple drag’n drop system.

Requires Icy 1.2 at least.

Track Processor computing the MSD (Mean Square Displacement).

Clip time processor for the Track Manager plugin

ROI Gate for the Track Manager plugin

Displays the Instant Speed of tracks for the Track Manager. This book chapter proposes a video tutorial on the Track Ma [..]

display the flows generated by a set of tracks in the Track Manager plugin

Track Processor to color tracks in the Track Manager

Tool to measure angle on images. Other plugins to measure angle: the Protractor plugin and the Angle Descriptor plugin. [..]

A protractor to measure angles on images

Widget to measure distances over images considering current image scale.

A set of classes and functions which can be used by plugins performing spot detection and spot tracking.

The track manager enables the use of DSP-like trackProcessors. This can affect the display of tracks, selection in time [..]

Manage a list of ROIs that the user can store and pop back in one click.

Create a list of tag and apply them to ROIs. Multi tag per ROI Tags are stored in sequence (persistent). Compatible wit [..]

Invert the image

Projects data over Z-Stack or over Time, using max, min, mean, sum saturated, and sum unsaturated. Sum saturated means t [..]

Spot detector detects and counts spots. – Detects spots in noisy images 2D/3D. – Depending on objective, spo [..]