Useful links
Photoquadrat and benthic image analysis | non-commercial software
An open-source software based on hierarchical segmentation algorithms to get semi-automatically segmented images from underwater photographs.
A Windows-based software for the determination of coral cover using transect photographs.
A public domain Java image processing program used to display, enhance, and analyze images, with additional tools for image calibration, area or distance measurements, as well as user-defined selections pixel statistics. You may also want to check out this site regarding the development of the next-generation version.
Analysis of species percent cover and density using point quadrat techniques. To download the software, go to the developer's webpage and look at the bottom of the page.
Other cool software tools
A Windows-based program for measurement of linear extension, density, and calcification from coral X-radiographs.
A software that integrates ImageJ and R statistical power for the development of individual-based or spatially explicit models.
A Python open-source software for quantitative phenotype measurement.
A software that enhances ImageJ by numerus plugins for image registration, segmentation, 3D reconstruction, and 3D visualization. If you're into cell biology or neuroinformatics, you'll find some interesting analysis and visualization plugins here.
A collection of ImageJ plugins and macros dedicated to microscopy analysis.
A community-based platform with many third-party libraries for 3D rendering and analysis of bio-images.
A 3D imaging software for visualization and analysis of multi-channel volumes.
