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Plugin List

Current number of plugins: 344

3
3D Active Mesh plug-in for cell segmentation and tracking in 3D images and sequences.
(1)
3D geometrical and shape measurements of 3D Area Rois (3D objects).
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SDK for 3D ROI creation and manipulation using polygonal (surface) and polyhedral (volume)...
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View 3D data in three orientations simultaneously (XY, YZ, XZ)
(4)
Takes the active 3D VTK viewer and records a 360-degree rotation of the data into a video ...
(4)

a
This plug-in implements fast active contours for image segmentation. Their representation ...
(4)
This plug-in implements fast active surfaces for 3D image segmentation. Their representati...
(2)
This is an icy package that encapsulates tools to design and implement parametric active c...
(1)
Automagically segment the boundary of a nucleus or cell starting from an approximate ROI. ...
(6)
The adaptive histogram equalization implements the Contrast-Limited Adaptive Histogram Equ...
(1)
Detects aggregates and export results to excel file.
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Tool to measure angle on images
(2)
This tutorial explain how to create an animated overlay.
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Generate nice dataset animations with interpolated camera points.
(2)
Anisotropic filter implements the classical Coherence Enhancing Diffusion Filter [Weickert...
(1)
Perona & Malik anisotropic diffusion for Icy, based on ImgLib2. An Icy plugin based on ...
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This plugin measures the percentage of elongated spots in a sequence.
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Simple tool to add annotations on your images.
(1)
The Apache Commons Mathematics Library: Commons Math is a library of lightweight, self-c...
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POI is a library dedicated to reading/writing Microsoft Office and compatible documents (W...
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use to slice array
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Overlay designed to be deformed to fit atlas over images
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Plugin Library used to provide autocompletion to JTextComponents, such as JTextArea or JTe...
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b
BactImAS: a platform for processing and analysis of time-lapse microscopy movies
(1)
Choose the best auto thresholding technique for your data. Ported from Auto Threshold plug...
(2)
Placeholder for a future plug-in
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Layer for 3D View that displays a Bounding Box around the object.
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BridJ library for Icy. https://code.google.com/p/bridj/
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c
The C-CRAFT software enables to segment particles and estimate background in 2D or 3D imag...
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The plugin provides tools to perform analysis of different types of calcium measurments in...
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This plugin detects and counts callose spots on plant materials.
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Build kymographs to monitor the evolution of the level of a liquid in capillary tubes
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View your multi-channel data as a montage with one image per channel plus a merged, color ...
(7)
Tutorial explaining how to display a JFreeChart graph in Icy.
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This tutorial explain how to use a deviation renderer JFreeChart chart in Icy.
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A canvas plugin using JFreeChart to show intensity profile of a specific row or column. In...
(2)
Simple chronometer for Icy.
(1)
This block can be used to filter ROIs as function of their circularity 2*pi*area/(perimete...
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Library used by Micro-Manager for fast acquisition.
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Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for hi...
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Creates a colocalization scatter plot based on 2 channels. This plugin can take 1 ROI as i...
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Create two synthetic sequences with given numbers of spots and colocalization properties (...
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This plugin contains most of existing colocalization methods in 2D and 3D fluorescence mic...
(2)
Colocalizer block. See colocalization protocol.
(2)
An extension of the Colocalizer block by fab which adds an extra output, 'Colocalization d...
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Display the colormap over the image using an overlay. Some settings are available as posit...
(2)
Image segmentation by representative colors selection. Two versions are available : - thr...
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This plugin allows to run javascript scripts from the command-line. It needs java 1.8 or h...
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This plugin permit to measure the signal spread of a molecule with respect to the cell are...
(2)
This plugin provides some useful functions to work with complex-valued sequences.
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Add a leyer on an image to display the detections
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This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and ...
(3)
Exports connected components data in XLS. Exports All, by T or by ROI
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The right click on sequences and ROIs will open a menu with various features, such as imag...
(3)
Draws a contour plot on top of a sequence.
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Creates convex versions of regions of interests in 2D or 3D using the QuickHull library.
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Select a portion of a sequence in all 5 dimensions (XYZCT)
(1)

d
Libraries for DICOM/DICONDE manipulation using dcm4che-2.0.27 from www.dcm4che.org. This ...
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Import DICOM/DICONDE file into Icy. This plugin is a part of EVA project, http://oeway.gi...
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A simple DICOM/DICONDE receiver used to recieve, store and open dcm images. This plugin i...
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This plugins allows debleaching of time sequences of fluorescence images.
(1)
This plugin / block allow to convert a DetectionResult object containing a set of Detectio...
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Input = Rois and Detections (viewed as ROIs) Output= Rois that contain at least one Detec...
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Some functions for PDE filtering
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Track Processor plugin that computes the relative distance between detections and their ev...
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Computes fast quasi-exact euclidean distance transforms in 2D/3D from a set of regions of ...
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This plugin allows fitting ellipses manually on an image. It can be used for generating go...
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Detect the position of flies placed into individual cages from a stack of time-lapse image...
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e
Align multidimensional images in 2D or 3D, rigidly or with warping, whatever the differenc...
(1)
Automatic registration in 2D or 3D based on detection or binary mask.
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Edge detection by Deriche's method.
(1)
This software smooth and denoise images while preserving sharp edges. The method relies on...
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View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).
(3)
Tracking plugin specifically designed for tracking of endocytosis/exocytosis in TIRF micro...
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EVA-Scanner is a plugin use Micro-Manager to control arduino GRBL board and PicoScope to c...
(1)
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a bandpass filter based FFT
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Draw the Envelope Line based on the Hilbert transform.Also works in protocols. The icon...
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*get the information of 1D singal in frequence domain ,also works in protocols
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Define feature extraction function in Jython or CPython (through Exenet)
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*get the feature of the MBN signal,like max,average,RMS,Ring num etc.
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This protocol collects 1D signal line to a multiline .Also can add labels
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Using DB wavelet to filter the signal noise,also works in portocols
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Open VarioCAM HD infrared camera image with "open" command in Icy. The extension is .irb a...
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EzPlug version of the imagej raw inporter, auto reload sequence when the parameters change...
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SAM File importer for PVA TePla Scanning Acoustic Microscope
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SAZ File importer for PVA TePla Scanning Acoustic Microscope
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Details how to listen and use events provided by the main interface.
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Shows how to listen active sequence / viewer events.
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Extrudes ROI along time, depth and/or channels to simplify manual segmentation and trackin...
(1)
The swiss army knife of plugin developers. Automatically generates elegant graphical inter...
(3)
Tutorial showing EzPlug\'s features in action. Check out the documentation to have a direc...
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f
Fast Fourier Transform (FFT) for 2D/3D images
(1)
Fast MultiThreaded 3D Filtering, use ellipsoidal neighbourhood, works for 5D images.
(1)
Icy Feature Detector plug-in implements a series of optimized contour and ridge detectors....
(2)
Simplify the 1D feature extraction task by exposing a simple feature extraction interface....
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Block creating a file name using the one of a sequence, adding text as suffix
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Fills holes below a given threshold. 3D data is currently processed slice per slice
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Fills the holes in all the ROI of the active sequence (also works in Protocols).
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Provides a selection of spatial, separable and customizable filters in 1D and 2D, with Ope...
(1)
This plugin allows fitting ellipsoids in 3D images rapidly. The author provides a few poin...
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Grab random images from Flickr : in recent uploads in interestingness st...
(2)
This plugin provides a painter to visualize 2D flows. 2D Flows are couples of two seque...
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Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.
(2)

g
Automatic detection of the variance (i.e. standard deviation, power) of the noise that aff...
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GcoPS is a non parametric and fully automatic plugin for colocalization analysis in 2D/3D.
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This plugin generates a bug in a thread, to show the capabilities of the automatic bug rep...
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This plugin is a test case for the automatic bug reporting feature in Icy. It generates an...
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This plugin generates 2D or 3D time sequences with elliptical objects moving over time in ...
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Creating in a few lines a plugin with an action button.
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Details how to create a custom GUI
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h
H2 database packaged as an Icy plugin See http://www.h2database.com
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Multi-Level 2D Undecimated Haar Wavelet Transform, including 1) decomposition of the input...
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The first hello world tutorial
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Compute and display the histogram of a sequence, with a more accurate control on the histo...
(2)
Enhances the global contrast by equalizing the histogram. This plugin transforms pixel...
(1)
This segmentation method performs a N-class thresholding based on a K-Means classification...
(1)

i
Performs tests and write a diagnose file that can be used to understand user problem and t...
(1)
Export your data from Julia to Icy. Server Part. see: https://github.com/Lightjohn/Julia...
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This tutorial details how to generate images of all differents types. (byte, int, short, u...
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Display a 2D sequence over another 2D sequence using additive blending
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A Protocols compatible Block that recieves and passes a sequence with 'inputImage' and 'ou...
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This tutorial focus on tools that Icy provides to easily process image data without having...
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convert a 2D Image to workbook
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Browse files in directories with thumbnails view
(5)
ImgLib2 wrappers for Icy. This library ships the tools needed to - wrap an Icy Sequen...
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Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugi...
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Plots an intensity profile of a given ROI. Can plot mean over T or/and Z too.
(3)
Intensity projection along depth or time with multiple algorithms: mean, max, median, vari...
(7)
An useful and cool painter plugin which displays the intensity profile of a roi within a r...
(2)
This plugin monitors your internet connection. The result image is updated every 5 second...
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Invert the image
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Generates tracks for benchmark.
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Compute a whole benchmark with all scenarios
(1)
TrackProcessor for the TrackManager plugin that allows importing/exporting tracks. Input a...
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Dedicated to score tracking dataset from the ISBI tracking challenge
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Reconstructs an isosurface from volumetric image data, and converts the surface into a 3D ...
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Isotropic wavelets transform for 2D images. The plugin provides a multiscale representa...
(1)

j
A tool to parse the javadoc of a file. Mostly used now by the Script Editor.
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JLargeArrays Library by Piotr Wendykier https://sites.google.com/site/piotrwendykier/so...
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JMathIO: easy to use read/write classes for double arrays. Written by Yann Richet.
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JMathPlot: interactive 2D and 3D plots. Library written by Yann Richet
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JMatIO is a library to open Matlab files. More info at https://github.com/gradusnikov/jmat...
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This plugin allows to use the JSC (Java Statistical Classes) library.
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JTransforms3 fft by Piotr Wendykier https://sites.google.com/site/piotrwendykier/softwa...
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Enables Python scripts that are run inside Icy to communicate with other Python instances ...
(1)
Supplementary material for the Jython engine (Lib, jline, jni, etc.).
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Python engine for Icy, based on Jython
(1)

k
Quantize a color image in any given number of colors.
(1)
This plugin allows the extraction of the kymograph representation of pixel intensity evolu...
(2)
A fork of Nicolas Chenourd KymographTracker plugin, made to play with kymograph filtering....
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l
Extracts labeled objects from a binary or labeled image into ROI using connected component...
(1)
Ligand-Receptor ratio quantifier
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A open-source utility library for linear programming in Java with the simplex algorithm. ...
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This tutorial explain how to retrieve informations about installed plugins.
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Snap image continiously, and enable you to change any property of camera during runtime
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Extract local extrema (maxima, minima or both) from a sequence.
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This plugin performs a laplacian of Gaussian filter in 3D. This can be useful to enhance b...
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2D viewer allowing to view image data in logarithmic scale. Useful to observe high dynamic...
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m
Ads a magnifier on top of the default 2D viewer to zoom in and inspect individual pixel va...
(3)
This plugin computes the Manders coefficients between ROIs in 2 sequences (Intensity and s...
(1)
Interactive counter. Click on the sequence to add detection, see number of detection in R...
(5)
Based heavily on the RigidRegistration plugin from Alexandre Dufour, this plugin allows re...
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Enable manual annotation of TNTs
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Like to do things old-school? Track your objects manually, the Icy way!
(3)
This plugin is designed to manipulate binary masks over images. It contains all the basic ...
(1)
Execute some simple math operations on sequences, such as addition, product, absolute valu...
(1)
Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequen...
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Import and export Icy sequences into Matlab .mat files within protocols.
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Low-level functions for interactive communication between Icy and Matlab. To use this p...
(2)
Export sequences from Icy to Matlab *.mat files.
(1)
Call Matlab functions from Icy.
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Import Matlab *.mat files as sequences in Icy.
(1)
Low-level library for reading and writing Matlab .mat files. This library also provides to...
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Use Icy as an image viewer from Matlab. This plugin provides an improved imshow functio...
(1)
Core Library developed by our lab for 3D image processing and analysis.
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The median filter remove the salt and pepper noise. The plugins works on 2D, 3D and 4...
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Cell membranes appear as structures of co-dimension 2, and suffer from discontinuities in ...
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Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned...
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This plugin allows the user to import Metamorph Rois into the Icy Software. The plugin is...
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Mice profiler temporal analysis of data
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Mice Profiler tracks multiple mice from a top view video.
(4)
Mice Profiler Video Label Maker processes tracking data to label a sequence thanks to a re...
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Allows to use Micro-Manager for Icy features inside Protocols.
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Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy ! Compat...
(1)
Used to be the micro manager libraries but now that is an empty plugin (provided for backw...
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Advanced Acquisition plugin for microscope.
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Manage all calibrators for your microscope.
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Calibrator for Pixel Size.
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Live video plugin for Micro-Manager for Icy.
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Display your data in real time 3D (depending on your hardware).
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Move your XY Stage and Focus Device with your mouse.
(1)
Snap complex images easily.
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Deprecated ! Use the new Micro-Manager blocks plugin.
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This plugin can display a 2D flow as a color-coded sequence, following the Middlebury colo...
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MitivDeconvolution is a deconvolution tool for widefield fluorescence microscopy that req...
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Displays 3D data as 2D montages of all slices.
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Morphomath operators: erosion, dilation, opening, closing, top-hat, gradient, distance map...
(4)
Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total di...
(4)
Unleash the power of your fingers and drag, rotate & zoom in your image using two-finger g...
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Multi-touch provider allowing developers to let their plug-in receive rich multi-touch int...
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This block plugin compute the intersection between the union of Rois 1 and the union of Ro...
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Takes rectangles, ellipses and polygons and generates a series of gradually smaller/larger...
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Tool for mycosis lung quantification
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n
A toolbox to chain image analysis processes
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A patched version of the Jama library. Internal structures accessors and package name a...
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My own toolbox used for all the plugins I developed.
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Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pe...
(1)
Non-linear filter implements the classical Perona-Malik PDE filter and the regularized ver...
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This plugin calculates the Nyquist sampling, in the radial and axial direction for your Mi...
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o
Official openBIS database integration plugin for Icy.
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Test plugin which performs computations on the GPU using the JavaCL library.
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OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org
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Set of utilities for OpenImadis servers (download, upload, annotate, with block processing...
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Import data from the Opera high-content screening system straight into Icy
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This plugin computes a displacement map from a sequence of at least two consecutive images...
(1)
An example of a very simple overlay.
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A slightly different painter than Overlay tutorial 1, focusing on canvas parameters instea...
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p
Creates an overlay on which you can draw. This can also be used to generate specific data ...
(1)
Provides easy-to-use yet powerful tools to automatically create realistic synthetic image ...
(1)
Simple particles animation. Up to 100 000 particles following the mouse cursor movement. ...
(2)
Shock Filter for image enhancement works on 2D, 3D or 4D sequence. implements the clas...
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PermuteAxis5D is a collection of tools to permute the axis of a 5D sequence. The plugin Pe...
(2)
Align pixels row by row according to specific threshold, originally used for surface track...
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Helps with measuring hue values from arabidopsis plantlets on dishes. This provides a neut...
(1)
Takes either a workbook of co-ordinates, or a ROI array as an input to generate 2D or 3D p...
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The plug-in is developed using a segmentation algorithm based on the Potts model. The user...
(2)
Projects data over Z-Stack or over Time, using max, min, mean, sum saturated, and sum unsa...
(2)
Design your own quantification protocol, visually. No programming required! Protocols can ...
(9)
Software Development Kit for the 'Protocols' programming environment
(2)
A protractor to measure angles on images
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This tool cuts existing ROIs by an angle using the graphical protractor tool. This plugin...
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PSF Generator is a software package that allows one to generate and visualize various 3D m...
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Additional operations for cell segmentation protocol
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Extracts Python files stored in plugins so that they can be used in Icy.
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This plugin allows to create an Icy plugin from a Python script, and produce a jar that ca...
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q
QuantEv is a generic and non-parametric framework that allows to visualize and quantitativ...
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QuickHull library for Icy. Computes convex envelopes of random point sets in 2D or 3D.
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r
A machine learning plugin uses RapidMiner, a powerful data mining software, to learn image...
(1)
This plugin provides tools for finite elements modeling on rectangular 2D grids. It pro...
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This plugin reloads all plugins without restarting Icy. It is especially useful when chang...
(3)
This plugin allows you to create a private repository to distribute your plugins and works...
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Rescale one or more ROI in a sequence about their center of mass
(2)
This library is used for JavaScript in the Scripting Editor. It is integrated in Java 6 & ...
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A simple tool for rigid registration of chromatic or temporal shifts, based on the Fast Fo...
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Creates ROI rings from existing ROI Each ROI are substracted by the first ROI of smaller ...
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Set of block (for graphical programming with Protocols) to perform different operations on...
(1)
Automatically assign a colour to each ROI of the sequence based on their perimeter
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This tutorial details how to process an image area defined by ROI.
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This tutorial explain how to create an intensity profile over an ROI.
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Calculates the number of objects (e.g. spots, bacteria etc.) inside larger objects (e.g. n...
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Compute and display the intensity evolution for regions of interests (ROIs) through time. ...
(4)
This plug-in activates keyboard shortcuts on the current viewer, allowing to move and copy...
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Manage a list of ROIs that the user can store and pop back in one click.
(1)
This tool compute measures on the ROIs of the chosen sequence, updates the measures live w...
(6)
Create a list of tag and apply them to ROIs. Multi tag per ROI Tags are stored...
(1)
This plugin / block allow to convert a set of ROI into a DetectionResult object containing...
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Block (Protocols) to convert ROI(s) into a binary image / sequence.
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Displays a live tool tip on the current focused ROI in an image. The tooltip displays t...
(1)
This tutorial explain how to create a simple Area ROI.
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ROIhelper is a plugin to help naming ROI. It adds all the names to a file and therefore wh...
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Widget to measure distances over images considering current image scale.
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s
Displays a scale bar overlay on the sequence. Be advised, this plugin needs correct Metada...
(4)
Take a screenshot of a 2D sequence with a custom magnification
(1)
This enables scripting in Javascript directly into a block.
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Create powerful scripts to implement what's missing with plugins. Syntax Color and Autocom...
(5)
This plugin allows one to use various basic sequence operations within Blocks.
(2)
This plugin provides a convenient interface to measure and compare the differences between...
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Save the data sequence as a series of CSV files,also works in protocols
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Plug-in for the Track Manager that loads (and saves) tracks from (to) the sequence metadat...
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This plug-in implements a user-friendly way to design shape-priors for the Active Cells pl...
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add, difference, etc between 2 sequences absolute value, inversion, etc. for 1 sequence
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Track one mouse from the top-view of a cage, using an MP4 input.
(1)
A simple painter showing the current Z position in a more classy version.
(1)
This plugin uses the Ripley's K function to analyze robustly the spatial organization of m...
(1)
Two-phase spherical parameterization algorithm for closed zero genus meshes.
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Use this tool to create Icy's splashscreens
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Splits regions of interest into smaller sub-regions based on size. This is useful to separ...
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Allows one to import spatio-temporal detections from a text file and also to export them. ...
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A set of classes and functions which can be used by plugins performing spot detection and...
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Spot detector detects and counts spots. - Detects spots in noisy images 2D/3D. - Depen...
(14)
This plugin ships automated methods for extracting trajectories of multiples objects in a ...
(5)
This plugin add blocks (Protocols) for the Spot Tracking plugin. These following blocks c...
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The SSIM is an index measuring the structural similarity between two images. It is valued ...
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Rotate the 3D stack from Front view to Right view or from Front view to Top view. ...
(1)
The plugin rotates each 2D image of the stack with a preset angle. The angle can be set f...
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SteerableJ
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Stereo vision support added to the 3D VTK canvas.
(1)
This is an icy plug-in that implements a stereo vision system. Renders 3D stacks simulatin...
(2)
AVADIS Image Management System is image database server developed by Strand Life Sciences ...
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AVADIS Image Management System is image database server developed by Strand Life Sciences ...
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AVADIS Image Management System is image database server developed by Strand Life Sciences ...
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This plugin allows visualizing the output of the structure tensor in 2D as a field of elli...
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This plugin allows visualizing the output of the structure tensor in 3D. A field of ellips...
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Substract all selected ROIs to all ROIs.
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This tutorial focus on how to send any type of data in the swimming pool.
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This tutorial focus on how to watch the swimming pool and get callback when an object is d...
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This plugin provides a color highlighting on text. Based on RSyntaxTextArea library of Fif...
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t
This plugin is the first stage of a cell tracking pipeline using parametric snakes. See th...
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It is a toy plugin to test semi-supervised texture segmentation using the new SLBPriu text...
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For each ROI, computes the number of pixel over a threshold. This plugin also provides the...
(1)
Extract image features based on one or more intensity thresholds, and output the result as...
(4)
Displays a customizable time stamp over a 2D sequence
(1)
The TiPi Library
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The track manager enables the use of DSP-like trackProcessors. This can affect the display...
(4)
Track Manager plugin that displays available tracks on the selected sequence, in both 2D a...
(3)
Track Processor to color tracks in the Track Manager
(2)
Display the track number on the viewer.
(2)
This processor exports the tracks in an xls file (compatible with Protocols)
(1)
This plugin was written to address a request from our lab. We had a t-stack of mitochondri...
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display the flows generated by a set of tracks in the Track Manager plugin
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display the Instant Speed of tracks for the Track Manager
(1)
A TrackProcessor that allows the user to monitor, visualize, and export, the intensity pro...
(3)
Track Manager module that calculates the time and duration of interactions between tracked...
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Track Processor computing the MSD (Mean Square Displacement).
(1)
ROI Gate for the Track Manager plugin
(1)
Clip time processor for the Track Manager plugin
(1)
Provides track length and track displacement using the sequence scale or arbitrary unit. A...
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Clip depth processor forTrack Manager plugin Show only the Detections in the range of c...
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Translate the tracks so that first detection is at 0,0,0 location
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TrackProcessor for the TrackManager plugin that allows computing several measures of trac...
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u
Reconstruct an image up to a desired scale, and do not add resulting residual.
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Library that detects the connection of USB drives (works on Mac, Linux and Windows)
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v
Deprecated: Use the Xuggler Video Importer plugin instead ! This plugin should import a...
(1)
Record what you are doing on a sequence as a .avi file, fully compatible with Icy.
(1)
This plugin shows how to display different type of 3D overlay in the VTK canvas 3D.
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w
This plugin implements the seeded watershed algorithm. It can be used for spots segmentati...
(1)
Detect envelope of waveform row by row, originally used in ultrasonic imaging.
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Wavelet Spot Detector for Blocks, to integrate in protocols.
(2)
Captures video from the webcam based on the Xuggler lib.
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Simple usage example for the Webcam Capture library.
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Webcam Capture library for Icy. This library allow easy access to webcam from Icy. You c...
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Displays and processes live webcam image using protocols. The processing protocol shoul...
(1)
This plugin generates the point-spread function (PSF) for a Widefield Fluorescence Microsc...
not rated yet
Toolbox to create and manipulate result tables with plug-ins and protocols, and export as ...
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Edit the workspaces with a simple drag'n drop system (Requires Icy 1.2 at least).
(4)

x
Tutorial on how to access single images in a video file. (Requires Icy 1.2.3)
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This plugin allows Icy to open many different video file format using the Xuggler library.
(1)

z
Manually explore 4D sequence to find the best z of interest, and construct the result sequ...
(3)
This is my first attempt at an ICY plugin. It is a rather simple tool that uses JAIs inter...
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Protocol List

Current number of protocols: 43

3
This protocol automatically quantifies the invasion rate of pathogens in a 3D tissue model. It calculates the ...

4
This protocol takes a folder with four channel images as an input and creates three separate three-channel ima...

a
2D or 3D automatic registration based on spot detection and on ECclem AutoFinder. Can serve as pattern search ...

b
Complete detection protocol with 3 outputs: excel, binary, and detection screenshot

c
This protocol will process a complete folder of image and automatically calculate the size of top object knowi...
This protocol counts the number of cells with signal aggregates in the neighborhood of cell nuclei (Golgi apar...
Display detections performed in 2 channels and colocalized detection.
This version automatically name the xls and binary output files
This protocol computes the Pearson and Manders coefficients between 2 spotty images (the masks of spots that a...
This protocol extracts the statistical percentage and distance of colocalization between 2 color molecule spot...
This protocol duplicates the input sequence as well as the ROI that are selected by the user
This protocol crops the input sequence to the bounding box of each ROI (thus producing a list of cropped seque...

e
This protocol will export statistics in excel format of all image available in a folder. If a ROI is present ...
Extract channels from a sequence to display or process them individually

f
This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and grows a co...

g
This protocol performs a smooth on the image.

i
This protocol uses a "folder loop" block to read every tif file in the specified folder and run an automated t...

l
This protocol saves series of a lif file as single tif file into a new folder named as the lif file. Series ar...
Allow the conversion of LSM files from a folder into TIFF files. Files are saved in the same folder.

m
This protocol compute the maximum Z projection for a whole folder of image (support multi serie image). By de...
Perform a median filter on the active sequence using the ImageJ rank filter plugin, and convert the result bac...
This protocol will do a single 2 channels image acquisition using Micro Manager for Icy.
This protocol will do a 3D Z stack image acquisition (2 channels) using Micro Manager for Icy.

n
This protocol ask for a nd file and convert all acquired series in individual sequence files. There are saved ...

o
This protocol computes the optical flow of a 2D+T sequence. The results are displayed with flow arrows pain...

p
PACT is aimed at dealing with large fluorescence microscopy datasets. It performs a first rough segmentation o...
For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.
Simple example to show how to iterate over all frame of a time sequence and process then independently.
This protocol, designed for the microbiology course at Institut Pasteur, allows to extract cell masks, and act...

s
This short protocol is an example to save a sequence with a modified name at the same hierachical level than t...
This protocol takes a folder containing images as input and extract each channel in a separate sub folder.
Simple protocol to change the pixel size information of all images contained in a folder.
Detects spots and save it in an excel file, in the same folder as the source file.
This is the first protocol with spot detection for test purposes.
This protocol allows detecting spots using wavelet spots detector plugin. It combines the wavelets spot detec...
This protocol shows how to use the new Spot Tracking blocks inside a Protocol. It does the following tasks : ...
This protocol allows detecting spots using wavelet spots detector plugin. It combines the wavelets spot detec...
This protocol allows detecting spots using wavelet spots detector plugin. It combines the wavelets spot detec...
This protocol counts the number of stained cells in a population of cells. It requires at least 2 color channe...
This protocol detects stress granules within cells using fluorescence imaging and quantifies their aggregation...

t
Just for testing
Threshold with multiple ROIs.xml
Detects and tracks cells in a 2D or 3D time-lapse sequence using active contours, and produces a list of ROI w...

Script List

Current number of scripts: 73

a
Access sequence width / height / channels / slices / time points.
Access pixel size and time interval on the sequence.
Adds a black channel to an existing sequence
This script creates a sequence with channel 0 and a new black channel. Combined with the painting plugin, the ...
This script will convert each sequence in a .lei/.lif file in individual Tif file. Convert sequences are reco...
This script shows how to resolve an Ambiguous error raised by JavaScript.
Displays the value of the angles along a polyline ROI.
Auto Thresholder using KMeans method. Based on Thresholder plugin.
Performs a threshold on the first channel of the image via the Otsu method, from BestThreshold plugin.

b
Batch process on a folder, using a K-Means algorithm for thresholding.
Use the Spot Detector and Spot Tracking plugin in a batch way (multiple movies directly loaded from a local lo...

c
Call a full macro from the script, and conversions between Icy and IJ.
Call an ImageJ Plugin from the Script.
Extracts channel 0 and 2 from a sequence and combine them.
Converts the image type
This script converts the ROIs of the active Sequence in a set of detection (DetectionResults) and export it in...
Converts a sequence time points to slices.
Converts sequence slices to time points.
Convert a sequence from a type to another.
Convert an image from a type to another.
This script takes the current active sequence and loop over its region of interest. For each ROI, it displa...
Creates a Dialog behaving like ImageJ macros'.
This protocol will iterate through all ROIs from the active Sequence and create for each ROI a new fixed size ...
Crop a sequence and copy the source ROI in the cropped sequence.
Crops a sequence.

d
This scripts takes a time-sequence as input. Then it use the spot detector for each image separately, using a...
This script is a modification of the script "Detect spot and change parameter along time" but it is using batc...
Detection script with post processing: box around mass center of each detection and display a ROI. Computes th...
Performs detection using WAT computation for each ROI independently. Practically, the script saves all the ROI...
Duplicates an image, to avoid altering data.

e
Simple example using loop roi and excel output
This script compute and exports the mean intensity and the standard deviation for a complete folder of image i...
Extract a single channel.
This script shows how to create a graphical user interface in Python, using the EzPlug SDK. Writing an Icy ...

g
Generate an image with specified width,height, number of channels and type.
Generates a polygonal ROI (5 points) and add it to the current sequence. Shows the use of points in scripting:...
Generates a rectangular ROI and add it to the current sequence. Shows the use of points in scripting: Point2D.
Generates various ROIs and add them to the current sequence. Shows the use of points in scripting: Point2D.
Generates a sequence and add it to the GUI. See also "Generate Image" script.
Creates a sequence with 100 time points, name it, and add it to the GUI.
Creates a sequence with 100 slices.
On a sequence with multiple ROIs, get the ROI of a specified index.
Get the selected ROI on the sequence.

i
Get an image from the current sequence. Add an image, then remove it.
Inversion of an ROI in python.

j
JMath Plot script

k
Performs a binary threshold using KMeans on an image smoothened with a Gaussian filter (kernel 3x3). Similar ...

m
This script shows how to use the Math Operation on two sequences, with a more advanced formula.
Example on how to use the Math Operations Plugin in scripts.
This script, measures the Mean Intensity in each ROIs in a GrayScale. you Must Open a picture file, select yo...
This script asks the user for an experiment folder produced by Axiovision and will create a multi-channel tiff...
Take an input folder containing several XLS files and merge them together while adding a new column containing...
Changes infos about pixel size and time interval on a sequence.
Move all selected ROIs together

o
Displays a File Selection Dialog to choose an image and open it as a sequence.
Displays a File Selection Dialog to choose multiple images and open them either as one or multiple sequences.
Usable on global view of a 96-Well Plates. It creates a grid of oval ROIs on the sequence and computes the mea...

p
This script allow you to export all pixels values which are contained in the ROI(s) into a excel file.
This script allow you to export all pixels values which are contained in ROI(s) into a excel file. Process is...
Computes if a point is inside an ROI or not.

r
Removes a channel from the sequence. See also Extract Channel.
Rename all ROIs of the active sequence
Sometimes, images metadata contains the same name, and thus are confusing for the user (two very different seq...
This script exports the ROI infos to an excel file. Here we just show it as an example for min, mean and max i...
Creates a grid of 100x100 Rectangular ROIs on a sequence.
Export the min / mean / max intensity of the selected ROI of active sequence over time in an excel file. The ...

s
Save the current sequence to the file selected by the user with a File Dialog.
Here is what this script does from an input image: - apply a gaussian filter to improve the segmentation -...
This script snaps an image with Micro-Manager.
Perform a snapshot and save the result into the selected file.

t
for test purposes only

u
Shows the different manners to create and access an Array in JavaScript.

v
This script illustrates how to adjust (some of) the camera parameters in a 3D VTK viewer