Automated

An example Clojure script illustrating how to run concurrent threads that perform independent tasks, and how to combine their results afterwards.

Produces files that allow individual batches of images to be processed separately on a cluster of computers.

FlipAndRotate flips (mirror image) and/or rotates an image

This module identifies objects that are contained within in a grid pattern, allowing you to measure the objects using Measure modules. It requires you to have defined a grid earlier in the pipeline, using the DefineGrid module. For several of the automatic options, you will need to enter the names of previously identified objects. Typically, this module is used to refine locations and/or shapes of objects of interest that you roughly identified in a previous Identify module. Within this module, objects are re-numbered according to the grid definitions rather than their original numbering from the earlier Identify module. If placing the objects within the grid is impossible for some reason (the grid compartments are too close together to fit the proper sized circles, for example) the grid will fail and processing will be canceled unless you choose to re-use a grid from a previous successful image cycle.

Displays a scale bar overlay on the sequence.
Warning: this plugin needs correct sequence metadata to be effective. Otherwise it will display wrong values.

Fiji Archipelago is a tool designed to make it easy for programmers to export Fiji/ImageJ functionality over a network to several other computers.

Color space conversions between image modes.

Via the RunImageJ module, CellProfiler can load images, run an ImageJ macro or plugin on them, and retrieve the results for downstream analysis via the RunImageJ module.

H2 database packaged as an Icy plugin

See http://www.h2database.com

DisplayDensityPlot plots measurements as a two-dimensional density plot.

Merges images from different columns to one image object as follows: the input images are regarded as one single line of pixels (depending on the iteration order of each underlying image factory). 

This tutorial details how to process an image area defined by ROI.