3D and 4D Real‒Time Interactive Image Visualization

Imaris 6.4

Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three-dimensional multi-channel images of any size. Conveniently load, process and visualize images acquired from almost any confocal or wide field microscope to gain new insight from your microscopic data. Communicate your results convincingly with our advanced movie generator and image export features. No other software gives you so much control at so many levels.

• Visualize volume images and objects in real time using a rich selection of rendering modes.
• Automatically or manually identify objects based on morphology, intensity, size and many more parameters.
• Validate segmentation by superimposing objects on the original volume image.
• Interact with individual objects.
• Create the most impressive pictures and animations with just a few mouse clicks.

The Imaris interface has been carefully designed for the life sciences. Imaris takes away the burden of selecting and managing multiple poorly integrated imaging tools and increases time spent on research. Imaris exploits the latest hardware technology to put new capabilities at your fingertips.

Datasheet

Image Handling

• Load an unlimited number of planes, channels and frames (z, c, t)
• Load 8/12/16/32 bit data
• Load data of any frame size and total size
• Adjust voxel sizes or time stamps if needed
• Automatically manage multiple resolution maps for each image
• Accurate yet fast display ensures one voxel is rendered per pixel on the screen for huge images
• Stitch image stack volumes to form a large multi-part image
• Use built-in data caching to disk (smarter and faster than OS caching) to efficiently utilize one or multiple high speed, low latency hard disks
• Cut processing time by utilizing multiple processors
• Interactively crop and/or resample on open (before data is read into memory)

Image Processing

• All functions operate on 2D, 3D, and 4D images
• 3D noise filters (gaussian, edge preserving, median)
• Basic and advanced thresholding (baseline subtraction, threshold cutoff, background subtraction, connective baseline)
• Contrast adjustments (linear stretch, gamma correction, inversion, local contrast detection)
• Channel adjustment and shifting (registration correction)
• Image rotation and flipping
• Custom image processing functions added through the ImarisXT module

Loaded Data Set Editing

• Visual 3D crop and time crop
• Add/delete slices, channels and/or time points
• Change dynamic range (8/16/32 bit per channel)
• Resample any dimension (increase or decrease)
• Adapt image origin to acquisition software (avoid flipping/ mirroring)
• Swap time/channel or time/planes to read reconstruct slices

Visualization - General

• Multi-resolution rendering to display huge images and keep visualization interactive
• Real-time contrast and brightness changes
• User-defined color palette or custom look up table (LUT) for each channel
• Selectively visualize any combination of channels
• Browse any view in 4D by moving the time slider
• Overall Image Display
  • Full‐Screen Mode — No toolbars
  • % Mode — Matches the screen and image resolution (one pixel per voxel)
  • Fit Mode — Enlarges the image to the maximum size that fits in the display window
  • Customize the zoom factor by manually entering the pixel / voxel ratio
  • Utilize the navigation window to determine the overall current viewing position relative to the entire dataset when at high zoom levels
• Classic views with real‐time zoom/pan
  • Customizable scale bar size, position, text size; accurately changes based on zoom level
  • Slicer View — inspect z‐sections and make precise measurements of voxel intensity on a per voxel basis
  • Section View — interactively see slices in x-y, x-z, or y-z at the same time, to perform extended focus visualization of a precise number of sections along any axis, or to render extended focus sections in maximum intensity projection (MIP), Mean or Blend modes
  • Gallery View — obtain an overview of all the sections or a selection of sections in the image, of all slices or selected slices
  • Easy 3D View — produce a fast maximum intensity projection (MIP) or blending projection

Visualization - Surpass View

• Layout
  • Orthogonal or customizable perspective viewing
  • Stereo rendering (red/cyan, interleaved, quad-buffered)
• Freely zoom, pan or fly through the image
• Real-time interaction and display
• Volume Object
  • Projection modes
    • Maximum intensity projection (MIP)
    • Alpha blending projection (Blend) with interactive transparency adjustment
    • Normal Shading — surface‐like rendering in which shadows occur away from the light source
    • Shadow Projection — blending with a shadow effect
    • Minimum intensity projection
  • Rendering Quality control improves speed on huge datasets or poor graphics cards
  • Apply lighting and color
• Surface Object
  • Apply lighting and color
  • Create/define multiple channels and thresholds
• Light sources
  • Define lighting, its position, color and intensity
  • Adjust position and intensity in real time
• Clipping planes
  • Cut away data or objects at any angle to reveal hidden information
  • Adjust position in real time at any angle with respect to the data set
• Orthogonal (Ortho) Slicer
  • View an orthogonal slice along the x-y, x-z, or y-z axis
  • Interactively move the slice in real time
• Oblique Slicer
  • Slice the data set at any angle or depth to view the data in that plane
  • Interactively move the slice in real time
• Utilize a frame or grid to show 3D scale (customize spacing, color, transparency, and labels)
• Import and visualize objects in the *.IV or *.WRL format

Interaction & Selection

• Select individual objects or multiple objects on a single screen in either the visual image view or the object list
• Intelligently select objects in 3D by automatically finding the correct depth location in a single mouse click via AutoDepth positioning and selection
• Utilize InMotion for smart selection and easy visualization of 3D positional information
• Group and classify objects of interest automatically based on image properties of individual objects or groups of objects
• Set any object as the center of rotation for the entire image
• Utilize InMotion for smart selection and easy visualization of 3D positional information:
  • Animation cueing rotates the whole image scene about the object under cursor
  • Stationary object cueing inserts reference points to easily see relationships between objects
• Combine InMotion and AutoDepth allowing selection of objects from the most complex images

Segmentation

• IsoSurface
  • Segmentation based on an intensity threshold
  • Segmented regions displayed as surfaces
  • Individual 3d objects treated independently
• Spot Detection
  • Automatic detection of local intensity maxima in 3DObject detection does not depend on intensity
  • Excellent for uneven staining or unevenly illuminated fields, bleachd or fading samples. and thick specimens
  • Excellent for touching objectsManual spot additions, deletions, or corrections possibleWorks on thousands or hundreds of thousands of objects
• Shaped Spots
  • Natural enhancement to spot detectionIntelligent seeded watershed
  • Accurately conforms segmented regions to objects true shape and size
• Masking
  • Utilize any surface object to include or exclude data in a segmented region
  • Apply the mask to any color channel

Microscopy File Format Compatibility

• Automatically extract and read original image data properties (if present in original file) including x, y, z voxel size, wavelight, channel names and look up tables, Numerical Apeture (NA), pinhole sizes, time stamps, and many other metadata fields

Microscopy Image File Loaders

• Confocal Formats
  • Carl Zeiss (LSM, AxioVision)
  • Olympus (FluoView, cell^R)
  • Leica (TCS-NT, LCS, LIF)
  • Biorad (MRC)
  • Nikon (ICS)
  • Perkin-Elmer (.zpo, .tim)
• Wide-field Formats
  • Applied Precision Inc. (DeltaVision)
  • BD Biosciences: IPLab
  • Molecular Devices: Metamorph
  • Till: TILLVisION
• Community image Formats
  • Open Microscopy Environment: (OME-XML, OME-Tiff)
  • Tiff series
  • BMP series
  • ICS/IDS
  • GIF, JPG, and PNG

Imaris File Converter

• Setup a list of files, and convert all of them into the Imaris 5.5 file format.
• The tool can also create other file formats

Output

• Snapshots:
  • TIFF image of any view in the program
  • Off-screen rendering for high resolution high-quality pictures
  • User defined snapshot size
• QuickTime VR of any or all objects in the Surpass view for interactive movies
• Movie Maker:
  • Simple and easy to use animation system
  • Create simple preset rotations or complex custom animations and flythroughs
  • Fast animation definitions using key frames by visually defining "key" positions and adding them
  • Smooth interpolation of camera position and time point
  • Control for object visibility, color, cntrast, brightness, transparency, clipping planes, and slicers
  • Control for movie length, speed, frames, and compression
  • AVI, MPEG, QickTime movie and TIFF series output
• File saving as Imaris, OME, Olympus Cell^R, ICS, BMP, TIFF series formats
• Scene saving of all objects in the object list to allow continuation of work at a later time
• Export Surpass objects as VRML or IV files

Operating System / Requirements

• Microsoft Windows 32 bit OS (NT, XP, 2000)
• Microsoft Windows 64 bit OS (XPx64, Vista)
• Macintosh OS X 10.3.9 or higher (Intel or Power PC processor)
• Open GL graphics board (see System Requirements for details)
• Ample RAM memory (see System Requirements for details)

Deconvolution references are available.