Automated

The Fiji Packager allows you to bundle an existing Fiji installation so you can share all the plugins and update sites with colleagues. It makes a single archive (.zip, .tar.gz, .tar.bz2 are supported at the moment) from the files in Fiji.app/.

Tutorial explaining how to display a JFreeChart graph in Icy.

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

Bundled with MBF pacakge.

PSF Generator is a software package that allows one to generate and visualize various 3D models of a microscope PSF. The current version has more than fifteen different models.

3D diffractive models: scalar-based diffraction model Born & Wolf, scalar-based diffraction model with 3 layers Gibson & Lanni, and vectorial-based model Richards & Wolf, and Variable Refractive Index Gibson & Lanni model.

Defocussing a 2D lateral function with 1D axial function: the available lateral functions are: "Gaussian", "Lorentz", "Cardinale-Sine", "Cosine", "Circular-Pupil", "Astigmatism", "Oriented-Gaussian", "Double-Helix".

Optical Transfer Function generated in the Fourier domain: Koehler simulation, defocus simulation.

This tool compute measures on the ROIs of the chosen sequence, updates the measures live when ROIs are changed and allows to copy/paste the measures to 3rd-party sheet edition softwares. Measures include geometric (bounding box) and intensity information.

It can complement the default ICY built inROI table, where measurements such as volume meausirements, intensity measurements, ... are built in and can be exported as excel as well.

This plugin calculates a classification based on the histogram of the image by generalizing the IsoData algorithm to more than two classes.

This plugin works on 8-bit and 16-bit grayscale images only.

A slightly different painter than Icy Overlay tutorial 1, focusing on canvas parameters instead of image parameters.

Python engine for Icy, based on Jython.

Required for: CalloseCounter, BioFlow, EvaFE In Python, Python Plugin Packager, Python Extractor, Jython execnet for Icy

Live video plugin for Micro-Manager for Icy.

This tutorial explain how to use a deviation renderer JFreeChart chart in Icy.

This plugin can display a 2D flow as a color-coded sequence, following the Middlebury color code.