BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images.
BioImageXD is a collaborative open source free software project, designed and developed by microscopists, cell biologists and programmers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG, Dresden, Germany and collaborators worldwide.
BioImageXD is written in Python and C++, using wxPython for the GUI, and leverages the power of the Visualisation Toolkit (VTK) for multi dimensional image processing and 3D volume rendering. BioImageXD also uses the Insight Toolkit, ITK for segmentation and other image porocessing tasks. BioimageXD works on Linux (or theoretically any UNIX with wxPython and VTK), Mac OS X 10.5, and MS Windows XP/2000 (possible Vista).
FEATURES
BioimageXD currently offers you, as a microscopy or other scientist, working with single or multi channel 2D, 3D or 4D (time series) image data
1.)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, Olympus, Leica and other commercial image viewers, but with very realistic 3D rendering without artifacts from the graphics card - using ray cast 3D mode. Viewing modes avaialble are: Slices, orthographic sections, maximum intensity projection and 3D rendering. Time series data are supported.
2.) 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.
3.) 3D VOLUME RENDERING
3D datasets can be interactively volume rendered, using :
i.)software ray casting (slower but prettiest. Accelerated by having many processors)
ii.)OpenGL graphics card texture mapping (faster but lower resolution - depending on texture menory size)
iii.)TeraRecon Inc. VolumePro1000 hardware ray casting board.
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.
4.) 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".
5.)Colocalisation analysis
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.
Click here to download this free software.
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