Track one mouse from the top-view of a cage, using an MP4 input.
This script takes the current active sequence and loop over its region of interest. For each ROI, it displays the num [..]
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 [..]
Simple example using loop roi and excel output
Interactive counter. Click on the sequence to add detection, see number of detection in ROIs directly over the sequence.
This script exports the ROI infos to an excel file. Here we just show it as an example for min, mean and max intensity for each ROI.
Detects spots and save it in an excel file, in the same folder as the source file.
for test purposes only
For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.
Crop a sequence and copy the source ROI in the cropped sequence.
Overlay designed to be deformed to fit atlas over images
Rename all ROIs of the active sequence
Compute a whole benchmark with all scenarios
Generates tracks for benchmark.
Threshold with multiple ROIs.xml
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
This version automatically name the xls and binary output files
Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.
Performs detection using WAT computation for each ROI independently. Practically, the script saves all the ROIs of a seq [..]
Displays a customizable time stamp over a 2D sequence
This scripts takes a time-sequence as input. Then it use the spot detector for each image separately, using a specific [..]
Complete detection protocol with 3 outputs: excel, binary, and detection screenshot
Converts the image type
Adds a black channel to an existing sequence
Detection script with post processing: box around mass center of each detection and display a ROI. Computes the sum of pixel.
Display detections performed in 2 channels and colocalized detection.
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.
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)
This is the first protocol with spot detection for test purposes.
Wavelet Spot Detector for Blocks, to integrate in protocols.
This protocol performs a smooth on the image.
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.
Mice profiler temporal analysis of data
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
display the Instant Speed of tracks for the Track Manager
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
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 [..]
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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 [..]