ImageJ is an adaptable image processing program that can deal with many digital images acquired from a modern research microscope and other biological image-aquisition apparatus. Documentation on the web can be found for almost any task a microscopist might wish to achieve with ImageJ. It will run on Microsoft Windows®, Macintosh, and Linux platforms.
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BioImageXD is another biomedical image manipulation program that is designed especially for multi-dimensional imaging, like time-lapse or 3d digital images. It will run on Microsoft Windows®, Macintosh, and Linux platforms.
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The Open Microscopy Environment is a project with the objective of creating a large suite of biomedical visualization and data manipulation tools. It is based on the client-server model, which could be helpful for the implementation of complex and computationally intensive data processing algorithms frequently used in biological imaging. If the project continues to proliferate, I expect it to become one of the most featureful and powerful open source biological imaging suites. Since it is mainly developed in java, it can also run on Microsoft Windows®, Macintosh, and Linux platforms.
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µManager is a complete image acquisition and microscope control package, easily interfacing with many research microscope models. It integrates directly with ImageJ for simultaneos image-aquisition and processing, and will work on Microsoft Windows®, Macintosh, and Linux platforms.
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The GIMP instantiates much of the same functionality as Adobe Photoshop®, though the implementation is slightly different. The application is able to enhance, manipulate, and create digital images in a variety of powerful ways. Plugins for the GIMP enhance and add to its functionality and many exist for a wide variety of imaging needs. The GIMP was originally designed for Linux systems, but has been ported to Microsoft Windows® and Macintosh systems as well.
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According to the Inkscape web site, inkscape is an Open Source vector graphics editor, with capabilities similar to Illustrator®, CorelDraw®, or Xara X®. Vector graphics are a kind of graphics represented as combinations of lines and shapes instead of pixels. This means they can be scaled to any size withouth any loss in clarity and without distortion. Such images are great for posters, publications, and other high resolution or very large printed and digital works. Ordinary bitmap images can be imported into inkscape, so it can be used to create diagrams and annotate images. It can also be used to make specialty graphics such as logos, posters, or even an entire pdf document.
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