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Free open source software for analysis and visualization of multidimensional biomedical images BioImageXD is a free open source software that will help you analyze, process and render multi dimensional, multi data channel, time series image data from microscopy and other sources. Here are some key features of "BioImageXD": Image Viewing: Open data in common microscopy formats (or images or stacks of images, and time series), and view the data image by image. Supported data formats include: · Carl Zeiss .lsm files · OlympusFV1000 .oif · Leica confocal microscope data files SP2 .txt and SP5 .lif · numbered image stacks import · VTK XML Image files · Image viewing is roughly comparable to the free Carl Zeiss and other confocal manufacturer image viewers, but with better 3D rendering. Viewing modes avaialble are: Slices, orthographic sections, maximum intensity projection and 3D rendering. Time series data are supported. Image processing: · Adjust colour / brightness / contrast / gamma, change colour or palette of a dataset/channel, filter out noise, correct for fluorescence bleaching in time series data. · 3D segmentation and object ananlysis. 3D volume rendering: · 3D datasets can be interactively volume rendered, using · software ray casting (slower but prettiest. Acellerated by having many processors) · OpenGL graphics card texture mapping (faster but lower resolution - depending on texture menory size) · TeraRecon Inc. VolumePro1000 hardware ray casting board (support in development) · The colour and opacity transfer functions are fully user defined. You can volume render a merged multi channel RGB dataset to see colocalisation in 3D, or render a 3D colocalisation map. BioImageXD uses the VTK interface with OpenGL. We plan to enable Hardware Stereo viewing (quad buffered page flipping and red-blue anaglyph, and other modes). You will be able to break out those 3D glasses and really "see" your data! This is the future of 3D microscopy. Movie making: · Use the Animator module to set up a camera path around your 3D data, and make a movie of it spinning and fly though zooming any way you like. Time series data are supported: "4D data". · Colocalisation analysis · We know all you cell biologists using confocal microscopy are always looking for colocalisation! Our colocalisation tool allows you to analyse the colocalisation of signal intensity in a multi channel 3D data set, avoiding the problem of false colocalisation seen in z-stack projection images, and perform some statistical analyses that give you hard numbers about the amount and quality of colocalisation in your data. Uses similar algorithms to those in imageJ, for instance the WCIF plugin for Automatic Colocalisation Thresholds, using the method of Costes et al. · Manders coefficients and statistical significance analysis, with 2D histogram/scatterplot and results statistics export

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