Molecular Research Core Facility

Image Analysis Station

This offline workstation includes multiple programs to help researchers analyze data generated from the Advanced Imaging Facility, and produce publication worthy images and pictures for various uses. Programs available on this computer are MetaMorph for Olympus, ImageJ (Fiji), Vaa3D - 3D Visualization-Assisted Analysis, Volocity Demo 6.1.1 and FluoRender. In addition to analysis software, the computer includes Microsoft Office and Adobe Reader.

MetaMorph® MetaMorph Applications
MetaMorph® for Olympus is an offline advanced digital imaging software for capture, display, and analysis of biological images. Built on the market-proven MetaMorph® platform, this powerful package offers functionality, flexibility, and stability that meet the most demanding image acquisition and analysis needs. MetaMorph® has been over cited in over 10,000 publications! Figure 1. Sample overlay of two images.
To better visualize events, up to six fluorescence images can be overlaid over a background Differential Interference Contrast (DIC) or phase contrast image.
  • 3D deconvolution and reconstruction
  • Angiogenesis/ Endothelial tube formation
  • Cell counting
  • Cell cycle and viability
  • Cell migration and proliferation
  • Colocalization
  • Cytotoxicity and apoptosis
  • Deconvolution
  • Densitometry
  • Fluorescence overlay
  • Fluorescence in situ hybridization (FISH)
  • Fluorescence immunocytochemistry
  • Fluorescence Recovery after Photobleaching (FRAP)
  • Fluorescence Resonance Energy Transfer (FRET)
  • Fluorescence
  • Intensity measurements
  • Live/Dead
  • Morphometry
  • Motion analysis & particle tracking
  • Mitosis
  • Monopole detection
  • Multi-dimensional imaging
  • Neurite outgrowth/ process extension
  • Ratio and calcium imaging
  • Receptor internalization
  • Stitching
  • Time lapse
  • Tissue imaging
  • Volume measurements
  • Z series
ImageJ (FIJI) ImageJ Applications
ImageJ is a public domain Java image processing and analysis program inspired by NIH Image. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and 'raw'. ImageJ supports 'stacks' (and hyperstacks), a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
  • Calculate are and pixel value statistics
  • Create density histograms and life profile plots
  • Geometric transformations; scaling, rotation, flips
  • Spatial calibration for real world dimensional measurements in units such as millimeters
  • User-written plugins make it possible to solve almost any image processing or analysis problem!
  • Measures distances and angles
  • Contrast manipulation, smoothing, edge detection and median filtering
  • Zooming up to 32:1, down to 1:32; including analysis at all magnifications
  • Density of gray scale calibration
  • Custom acquisition, analysis and processing plugins can be created with Java compiler
Vaa3D Vaa3D Applications
Vaa3D is a handy, fast, and versatile 3D/4D/5D image visualization and aalysis system for bioimages and surface objects. It also provides many unique functions. It is also open source, supports a very simple and powerful plugin interface and thus can be extended and enhanced easily.
  • Intensity projections
  • Alpha blending
  • Cross-section view
  • Real time 4D blending, multi-color channels
  • Co-localization
  • 3D quantitative measurements
  • Other plugins available
  • Surface 3D cut
  • Color-mapping of voxels and recoloring of surface objects
  • 3D pinpointing
  • Animation and movie making
  • 3D neuron tracing, landmarking, surface mesh generation
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Figure 2: Use of Vaa3D in visualizing a digital mode of a fruitlfly brain. Magenta voxels: the 3D volumetric image of a fruitfly brain; green voxels: a 3D GAL4 neurite pattern; colored surface objects of irregular shapes: digital models of various brain compartments; colored tree-like surface objects: 3D reconstructed neurons. (Myers et al. 2010, Nature Biotechnology.)
Volocity® Demo 6.1.1 Volocity Applications
Volocity® is the universal solution for 3D analysis of fluorescence microscopy images. A collection of high performance 3D imaging software products, Volocity® lets you turn images into understanding, relate cellular structure to function and deliver quantitative measurements for publication.

Volocity® Demo is a fully functional version of Volocity® 3D analysis software that allows you to interact with your 3D images, and test and evaluate the software's analysis capabilities in your own time and on your own computer - for an unlimited period.

Figure 3: 3D visualization by Volocity of and image captured using a confocal microscope.
  • Drag and drop your image files into the software to interactively explore in 3D
  • Rotate, zoom and fly through rendered objects in real time
  • Choose from rendering options including solid surfaces, varying opacity and shadows
  • See how the three dimensions intersect at any point
  • Explore structures and processes from any angle in fixed and dynamic experiments
  • Prepare stunning images and movies for publication and presentations
FluoRender FluoRender Applications
FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, and it helps them better visualize the fluorescent-stained confocal samples. Figure 4: Sample data from FluoRender
  • Multiple render modes for multi-channel confocal data.
  • Rendering properties of individual channels can be adjusted independently.
  • Intuitive and easy-to-use parameter adjustment enhances workflow efficiency.
  • Easy generation of animations and movie exporting.
  • Trimming of individual channels with clipping planes.
  • Data channels can be grouped. Gamma and brightness can be set independently for each group in layered and composite modes.
  • 4D time sequence data support.
  • 3D batch rendering for RGB TIFF files.
  • Scalar value dependent colormap.
  • RGB and 16-bit grayscale multi-layer TIFF file format support.
  • Maximum Intensity Projection (MIP) supported.
  • Clipping planes can rotate independent of the object.
  • Equalization for 3D and 4D confocal data.
  • Shadow effects.
  • Volume paint selection and segmentation.
  • Better support of Zeiss format, including larger-than-4GB data support.


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