Features Here is what BioimageXD currently offers you, as a microscopy or other scientist, working with single or multi channel 2D, 3D or 4D (time series) image data: | Feature | Description | | 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.
| | 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 | Future development We are actively developing BioImageXD and plan to add and enhance lots of functions. If you have suggestions for features or GUI improvements, or bug reports, email us at
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. Here is a list of features that we plan on adding in the months and years to come (items are listed in no specific order): | Feature | Description | | Native reading of Olympus, BioRad/MRC, and other confocal microscope data formats | We have all sorts of exotic microscopes, so we need to open that data in BioImageXD! Lots of people have Metamorph controlled microscopes. We are working on a reader. (Sample data files and the file format specifications for your unsupported microscope system are very helpful if you have them! Please contact
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if you can assist us in this.) | | Devonvolution | Remove out of focus signal from confocal microscopy image data using deconvolution. Reducing the blurring effects of the non-point nature of the point spread function used in imaging. Might be simple to implement basic deconvolution using a calculated or measured psf, but might not give high quality results. | | Spectral unmixing | Remove components of spectral mixing from images, to make colocalisation studies more reliable when fluorophore emmissions overlap in data channels. Algorithms are published that we could implement. (any suggestions?) | | Distance, Area, and Volume measurement and Particle Tracking tools | Some kind of point to point measurement tool, working in 3D. Region of interest registration/segmentation in 3D. Calculation of volumes, eg volume of a cell/nucleus/compartment/etc. Identiftying and tracking the movements of objects in time series data. Identification and analysis of proximal particles. Adjacent blobs in differetn channels that don't overlap, but are next to each other. | | AFM image viewing | Atomic force Microscopy and related imaging techniques make images that can be rendered as 3D surfaces. We can also add some useful image filters and the like. Maybe have some kind of AFM shape - PDB or cryoEM structure/model fitting tool. Comaprison of cell surface height images with confocal 3D datasets. | | CryoEM data viewing | Cryo Electron microscopy produces volume-density datasets, which can easily be 3D volume rendered with VTK. Very good for interactive exploration of your density! And making movies etc. | | Advanced graphics hardware features | Hardware Stereo. 3D texture mapping volume rendering. VTK is beginning to support OpenGL pixel and vertex shaders, so these could ber used to speed up hardware accelerated volume rendering on modern (nVidia?) graphics cards. | | Multiprocessor, parallel computing, clusters and supercomputers | As part of the FinHPC project we plan to enable BioImageXD to run image processing and other functions in parallel and with CPU specific vectorised code (Altivec/velocity engine on G4 and G5, and MMX SSE SSE2 SSE3 on ix86), on desktop computers, clusters, workstations, servers, and super computers with large shared memory | | Your feature request here! | If you have a feature request, or some image processing algorithm suggestions, or whatever else... we can try to implement those. BioImageXD is mainly written in python, so new features are fast and easy to add. If speed is importent, then we can use c++. |
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B i o I m a g e X D
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