Resources

Yes, it is finally here. A user-friendly interface to Docker, letting you run containers within your plug-ins in no time.

Created on: 11 Sep 2017
No reviews
Modified: 27 May 2021

Protocol measuring the cellular internalisation rate of chlamydia based on two fluorescence reporters (one for all bacte [..]

Created on: 25 Apr 2017
No reviews
Modified: 08 Apr 2021

Calculates the number of objects (e.g. spots, bacteria etc.) inside larger objects (e.g. nuclei, cells etc.), as well as [..]

Created on: 26 Aug 2016
2 reviews
Modified: 27 May 2021

Import data from the Opera high-content screening system straight into Icy

Created on: 20 Apr 2016
No reviews
Modified: 14 Sep 2020

JMathPlot: interactive 2D and 3D plots. Library written by Yann Richet

Created on: 17 Mar 2016
No reviews
Modified: 17 Mar 2016

JMathIO: easy to use read/write classes for double arrays. Written by Yann Richet.

Created on: 17 Mar 2016
No reviews
Modified: 17 Mar 2016

Splits regions of interest into smaller sub-regions based on size. This is useful to separate clustered objects.

Created on: 08 Mar 2016
No reviews
Modified: 26 Sep 2017

This script asks the user for an experiment folder produced by Axiovision and will create a multi-channel tiff file from the separate channel files.

Created on: 29 Jan 2016
No reviews
Modified: 29 Jan 2016

JMatIO is a library to open Matlab files. More info at https://github.com/gradusnikov/jmatio

Created on: 14 Dec 2015
No reviews
Modified: 21 Dec 2015

This plug-in activates keyboard shortcuts on the current viewer, allowing to move and copy regions of interest (ROI) in [..]

Created on: 29 Jul 2015
No reviews
Modified: 31 Jul 2015

Reconstructs an isosurface from volumetric image data, and converts the surface into a 3D region of interest.

Created on: 29 Jul 2015
No reviews
Modified: 23 Aug 2016

OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org

Created on: 23 Apr 2015
No reviews
Modified: 14 Jun 2021

SDK for 3D ROI creation and manipulation using polygonal (surface) and polyhedral (volume) meshes.

Created on: 24 Nov 2014
No reviews
Modified: 27 May 2021

Track Manager plugin that displays available tracks on the selected sequence, in both 2D and 3D viewers, with various vi [..]

Created on: 16 Oct 2014
3 reviews
Modified: 27 May 2021

Plug-in for the Track Manager that loads (and saves) tracks from (to) the sequence metadata. Your tracking data will never be lost again!

Created on: 24 Jul 2014
No reviews
Modified: 24 Jul 2014

Creates convex versions of regions of interests in 2D or 3D using the QuickHull library.

Created on: 04 Mar 2014
No reviews
Modified: 27 May 2021

QuickHull library for Icy. Computes convex envelopes of random point sets in 2D or 3D.

Created on: 04 Mar 2014
No reviews
Modified: 27 May 2021

Extracts labeled objects from a binary or labeled image into ROI using connected component analysis

Created on: 23 Jan 2014
1 review
Modified: 21 Sep 2021

Extrudes ROI along time, depth and/or channels to simplify manual segmentation and tracking

Created on: 12 Dec 2013
1 review
Modified: 12 Dec 2013

Rescale one or more ROI in a sequence about their center of mass

Created on: 07 Nov 2013
3 reviews
Modified: 27 May 2021

Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for high-fidelity color printing)

Created on: 02 Jul 2013
No reviews
Modified: 12 Jan 2016

Automatically assign a colour to each ROI of the sequence based on their perimeter

Created on: 13 Jun 2013
No reviews
Modified: 13 Jun 2013

Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a block for Protocols

Created on: 10 Jun 2013
No reviews
Modified: 27 Feb 2017

Detects and tracks cells in a 2D or 3D time-lapse sequence using active contours, and produces a list of ROI where inten [..]

Created on: 12 Mar 2013
No reviews
Modified: 09 Jun 2015

Perform a median filter on the active sequence using the ImageJ rank filter plugin, and convert the result back into Icy for display

Created on: 08 Mar 2013
No reviews
Modified: 08 Mar 2013

Toolbox to create and manipulate result tables with plug-ins and protocols, and export as text file or to your favorite spreadsheet software

Created on: 11 Jan 2013
No reviews
Modified: 13 Jul 2021

This protocol crops the input sequence to the bounding box of each ROI (thus producing a list of cropped sequences), and [..]

Created on: 07 Nov 2012
No reviews
Modified: 07 Nov 2012

Ads a magnifier on top of the default 2D viewer to zoom in and inspect individual pixel values

Created on: 22 Oct 2012
3 reviews
Modified: 27 May 2021

Fills holes below a given threshold. 3D data is currently processed slice per slice

Created on: 10 Oct 2012
No reviews
Modified: 22 Jul 2013

View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).

Created on: 09 Aug 2012
3 reviews
Modified: 23 May 2016

Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total displacement (absolute & rel [..]

Created on: 08 Aug 2012
4 reviews
Modified: 27 May 2021

Takes the active 3D VTK viewer and records a 360-degree rotation of the data into a video sequence.

Created on: 02 Aug 2012
5 reviews
Modified: 27 May 2021

3D Active Mesh plug-in for cell segmentation and tracking in 3D images and sequences.

Created on: 10 Jul 2012
1 review
Modified: 27 May 2021

Select a portion of a sequence in all 5 dimensions (XYZCT)

Created on: 30 Mar 2012
1 review
Modified: 03 Sep 2012

2D viewer allowing to view image data in logarithmic scale. Useful to observe high dynamic range images, e.g. Fourier spectra or 16-bits images.

Created on: 21 Dec 2011
No reviews
Modified: 22 Jun 2016

Unleash the power of your fingers and drag, rotate & zoom in your image using two-finger gestures (in 2D and 3D)

Created on: 22 Sep 2011
No reviews
Modified: 22 Apr 2013

Multi-touch provider allowing developers to let their plug-in receive rich multi-touch interaction. Currently supports M [..]

Created on: 19 Sep 2011
No reviews
Modified: 22 Apr 2013

Intensity projection along each of the 5 sequence axes (X, Y, C, Z, T), with multiple algorithms: mean, max, median, var [..]

Created on: 20 Jul 2011
7 reviews
Modified: 27 May 2021

This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then [..]

Created on: 19 May 2011
1 review
Modified: 17 May 2021

Extract image features based on one or more intensity thresholds, and output the result as a labeled image or as a region of interest.

Created on: 29 Apr 2011
4 reviews
Modified: 23 Jun 2021

Test plugin which performs computations on the GPU using the JavaCL library.

Created on: 15 Mar 2011
No reviews
Modified: 22 Oct 2012

Tutorial showing EzPlug's features in action. Check out the documentation to have a direct view of the code

Created on: 28 Feb 2011
No reviews
Modified: 20 Feb 2012

This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works [..]

Created on: 25 Jan 2011
3 reviews
Modified: 27 May 2021

The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive [..]

Created on: 21 Jan 2011
3 reviews
Modified: 21 Sep 2021