Segmentation (Image Processing) - Important Concepts in Signal Processing, Image Processing and Data Compression - page 37

Proprietary software

Several proprietary software packages are available for performing image segmentation

Pac-n-Zoom Color has a proprietary software that color segments over 16 million
colors at photographic quality.

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TurtleSeg is a free interactive 3D image segmentation tool. It supports many
common medical image file formats and allows the user to export their
segmentation as a binary mask or a 3D surface.

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Open source software

Several open source software packages are available for performing image segmentation

ITK - Insight Segmentation and Registration Toolkit (Open Source)

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ITK-SNAP is a GUI tool that combines manual and semi-automatic segmentation
with level sets.

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GIMP which includes among other tools SIOX

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VXL

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ImageMagick

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3DSlicer

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MITK has a program module for manual segmentation 

OpenCV is a computer vision library originally developed by Intel.

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GRASS GIS has the program module i.smap for image segmentation

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Fiji - Fiji is just ImageJ, an image processing package which includes different
segmentation plug-ins.

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AForge.NET - an open source C# framework.

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There are also software packages available free of charge for academic purposes:

GemIdent

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CVIPtools

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MegaWave

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Benchmarking

Prague On-line Texture Segmentation Benchmark - enables comparing the
performance of segmentation methods with the state-of-the-art segmentation methods on
a standardized set of textured images