| Allen Cell Explorer | Fast and versatile 3D/4D/5D Image visualization and analysis system for bioimages and surface objects. Extracts complex surface objects from images, and performs comprehensive analyses such as brain connectome mapping. |
| BioImageXD | Open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. Collaborative project, developed by microscopists, cell biologists and software engineers. |
| CellOrganizer | Constructing generative models of the organization of cells, and generating synthetic images or movies of cells using those models. |
| CellProfiler | Cell/particle counting, and scoring the percentage of stained objects. Yeast colony classification. Imaging Flow Cytometry. C. elegans worm image analysis. |
| FARSIGHT | Toolkit of image analysis methods to enable quantitative studies of complex & dynamic tissue microenvironments that are imaged by modern optical microscopes. |
| FIJI | ImageJ bundled with a lot of plugins which facilitate scientific image analysis. |
| ITK | Open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. |
| Icy | Open community platform for bioimage informatics. Popular plugins: Spot detector detects and counts spots. Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total displacement. Stereo viewer renders 3D stacks simulating a dual view camera. |
| ImageJ | Java image processing program. Supports smoothing, sharpening, edge detection, median filtering and thresholding on both 8-bit grayscale and RGB color images. Interactively adjust brightness and contrast of 8, 16 and 32-bit images. Measure area, mean, standard deviation, min and max of selection or entire image. Measure lengths and angles. Can display and process confocal microscopy LSM images and z-stacks. |
| OpenCV | Open Source Computer Vision Library. |
| VCell | Platform for modeling cell biological systems that is built on a central database and disseminated as a web application. |
| VolViewer | Real-time volume rendering for viewing volume images from, for example, confocal microscopy or optical projection tomography (OPT). |
| ilastik | User-friendly tool for interactive image classification, segmentation and analysis. |
