Israel Science and Technology Directory

Biomedical Software

Cell Imaging Software
BioImageXDOpen source software package for analyzing, processing and visualizing multi-dimensional microscopy images. Collaborative project, developed by microscopists, cell biologists and software engineers.
CellOrganizerConstructing generative models of the organization of cells, and generating synthetic images or movies of cells using those models.
CellProfilerCell/particle counting, and scoring the percentage of stained objects. Yeast colony classification. Imaging Flow Cytometry. C. elegans worm image analysis.
FARSIGHTToolkit of image analysis methods to enable quantitative studies of complex & dynamic tissue microenvironments that are imaged by modern optical microscopes.
FIJIImageJ bundled with a lot of plugins which facilitate scientific image analysis.
ITKOpen-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.
IcyOpen 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.
ImageJJava 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.
OpenCVOpen Source Computer Vision Library.
VCellPlatform for modeling cell biological systems that is built on a central database and disseminated as a web application.
Vaa3DFast 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.
VolViewerReal-time volume rendering for viewing volume images from, for example, confocal microscopy or optical projection tomography (OPT).
ilastikUser-friendly tool for interactive image classification, segmentation and analysis.