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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.

Color space conversions between image modes.

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

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

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.

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

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

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