Imaris

Imaris is Bitplane’s core scientific software module that delivers all the necessary functionality for data management, visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size.

  • Search, tag, and manage your data
  • Organize and manage full experiments
  • Premier Volume Rendering
  • Spots and Surfaces, Segmentation and Interaction
  • Interactive, Intuitive; Navigation and Selection

3D and 4D Real-Time Interactive Data Visualization and Management

Imaris enables you to manage all your image data, image analysis protocols, results and derived data. The Arena view also enables you to tag your resources (e.g. images) as well as intelligently search across all experiments or a specific set of experimental groups. Imaris’ Surpass view allows for the visualization of original and derived data objects in a real time and interactively so you can quickly make visual assessments of your experiments in 3D and 4D to discover relationships that are otherwise hidden. Its rendering quality, speed, precision and interactivity are unrivalled. With a large variety of segmentation options, Imaris provides you with the most effective tools to segment even the toughest datasets to identify, separate, and visualize individual objects and then utilize the Imaris MeasurementPro module to pull out the derived measurements.

Imaris includes features to communicate and share results convincingly: The "Snapshot" command is a convenient way to export any image view in a standard format that can be used for presentations and publications. The highly advanced “Key Frame Animator” allows intuitive creation of even the most complex movie from 3D and 4D scenes. No other software gives you so much control at so many levels.

  • Organize and manage all image data related resources (e.g. raw data, segmented results, image analysis protocols)
  • Search all (or part) of your image related resources
  • Tag resources
  • 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 dynamically with individual objects
  • Create the most impressive pictures and stunning animations for your publications and presentations 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 technologies to put new capabilities at your fingertips.

Since its launch in 1993 Imaris has been installed at hundreds of leading sites throughout Europe, America, and Asia. Imaris has been chosen as the primary tool for image visualization and analysis by individual investigators, core facility managers as well as operators of our Advanced Imaging Centers.

Data Management, Searching and Tagging

  • Data Management - From version 8.0 Imaris includes the Arena view – a powerful and fully integrated data management system, powered by the open source project BisQue.
  • Storage - Imaris Arena enables storage of its data organization structure with all of your datasets on a network or local drive.
  • Searching - From within the Arena view one can search for file names, tags and metadata. Searches can take place across all experiments, a group of experiments or a sub-group within an experiment.
  • Tagging - Text tagging gives you flexibility when organizing your data and results.
  • Batch Analysis - Organize and trigger the batch analysis of multiple images using a pre-defined image analysis protocol within the Arena view. Batch analysis can be done on all images of one group or all images from multiple groups. The results of a Batch job can directly displayed and explored in Imaris Vantage. Performing the Batch analysis requires the Imaris Batch module
  • Comparison Vantage Plot - Easily create a comparison plot (e.g. control group vs treatment group). With a few clicks one can generate an interactive uni- or multi-variant plots comparing the results from groups of images – an ideal method for exploring results and testing hypothesis. Creating plots requires the Imaris Vantage module.

Premier Volume Rendering

Imaris contains multiple high-class volume rendering algorithms to produce exceptional 3D and 4D images.

  • MIP (Maximum Intensity Projection) - This projection is implemented in Imaris so that even the largest datasets can be interactively rotated in 3D or 4D space.
  • Blend Projection – Weights the data that is closer to the viewer, so that on a 2D screen the viewer can get a more realistic 3D impression of the data set and the depth relationship of the objects being viewed.
  • Real-Time Shadow Rendering - The fast hardware driven shadow projection can produce shadows on the three planes of the “Frame Object” to enhance the realism of the images and introduce additional depth perception.
  • Normal Shading – Similar in appearance to surface rendering, “Normal Shading” does not require the computation of a triangle mesh. Instead it computes the orientation of the virtual surface from the voxels directly and uses this information to shade the surface appropriately. This allows you to carry out fast and flexible surface rendering for very large datasets
  • Display Adjustment – The intensity for each color channel in the image can be interactively adjusted in real-time to eliminate background noise and to brighten the image. The gamma for each channel can also be interactively adjusted. For rendering techniques that utilize transparency, this characteristic can also be changed in real time.

Surfaces, Segmentation and Interaction

The Surface Object is a computer-generated representation of a specified region of interest in the data set. This surface object is visualized as an artificial solid object, and allows you to verify the accuracy of segmentation against the original data in an interactive manner. The surface object acts as a container from which statistics can be calculated with the Imaris MeasurementPro module. Surface Objects can also be tracked with the ImarisTrack module. Surface objects can be generated in the following ways:

  • Automatic Iso-Surfaces – Surface Objects are created based on an intensity value on a per channel basis. Selection of the intensity threshold is completely interactive.
  • Automatic Local Contrast Surfaces – Surface Objects are created based on the contrast in the area around the object. This allows the accurate selection of objects where the overall intensity may vary within the depth of the image or over time. Selection is completely interactive.
  • Automatic Region Growing – Surface Objects are created by first identifying a region to look in for the objects of interest using either the local contrast or iso intensity methods, then Seed Points are calculated to mark each individual object. The result is that complex images, where the out of focus light overlaps between what should be separate objects, can have the objects split apart and treated individually.
  • Retain various sets of surface creation parameters – Save and remember surface object creation parameters to use identical settings for analysis of another data set.
  • Surface Scissors - Manually split two touching Surface Objects along an interactively specified cutting plane. One click separates the objects.
  • Semi-Automatic Surface Generation – The Magic Wand allows automatic global surface creation based on a manually selected ROI. The Marching Cubes algorithm allows automatic surface additions only in selected local regions.
  • Surface Visualization – Surface Objects can be visualized with the original data for verification purposes. The Surface Objects can be colored in any desired color, color-coded according to any desired measurements and given visualization properties for shininess and transparency. Color properties can be selected from a predefined color palette or can be custom designed and saved for future use.

Spots, Segmentation and Interaction

The Spot Object is available to model point-like or vesicle-like structures in the data. Like the Surface Object above, a Creation Wizard guides the user through the step-by-step procedure to automatically detect point-like structures, an editor to manually correct detection errors if necessary, and a viewer to visualize the point-like structures as spheres. The advantage of the Spot Object is that local maxima can be identified and images with 10’s or 100’s of thousands of objects can be quickly identified individually.

  • Spots – Like the Surface Object the Spot Object is an artificial object allowing the comparison between the original data and what has been segmented. Like the Surface Object, the Spot Object acts as a container from which statistics can be calculated with the Imaris MeasurementPro module and tracking can be performed with the ImarisTrack module. The difference between a Spot Object and a Surface Object is that a Spot Object is always spherical or ellipsoidal in Z, but can vary in diameter.
  • Automatic Creation of Spots - Spherical models of objects can be created automatically based on the approximate size of the object regardless of the overall intensity. This is ideal for images that have attenuation of intensity in Z or over time where pure intensity based methods fail.
  • Manual Creation of Spots – Spots may be manually added or deleted in any image in 3D or 4D by simply moving the mouse over an object and clicking. This allows for quick and easy editing if automatic detection has problems or for the possibility to do the work completely manually. Imaris assists the user with spot placement by automatically detecting the correct depth to place the spot into the screen saving the user tremendous amounts of time. When combined with InMotion, object identification and segmentation that previously took hours is completed in minutes.
  • Retain various sets of spots creation parameters - Save and remember Spot Object creation parameters to use identical settings for analysis of another data set.
  • Visualization of Spots - Spots can be visualized together with any of the other available objects and with the original data. The Spot Objects can be colored any desired color and given visualization properties for shininess and transparency.

Interactive, Intuitive; Navigation and Selection

  • Advanced On-Line Interaction With The Object – Rotate, zoom in and out and fly through the Volume in real-time.
  • Kinetic Depth Effect - Imaris offers a series of motion animation and depth cueing tools that are unique in the microscopy market and enhance 3D interaction. InMotion introduces stationary or animated visual elements into the visual data scene to provide a structured frame of reference if needed. The InMotion function allows the user to accurately visualize and easily select data in even the most complex 3D or 4D images.
  • Navigation Window – A Navigation Window displays an overview of the data set in the Surpass View. While exploring datasets, you will never be lost because as you move within the data set the overview image updates in real-time.
  • Filtering - Filtering is incorporated into the creation process of Surface Objects and Spots Objects enabling the composition of filters consisting of several measurements and interactive visual feedback on parameter selection.

Smart Handling of Huge Images

Imaris provides smart handling of huge data sets (50GB or more), that exceed the available main memory, e.g. on computers with only a small amount of RAM. This allows for the processing of images in Imaris where other programs completely fail.

  • Block-Wise Paging – The handling of huge data sets is based on the principle that only the parts of the dataset and the resolution of the dataset needed for the actual view are loaded to RAM and displayed. This principle makes the most efficient use of RAM memory space.
  • Processing - Load, open and render huge images instantaneously and easily. If the computer system has multiple hard disk drives, Imaris can use all of them in parallel to transfer data that cannot be held in RAM or graphics memory. This results in improved performance for the largest datasets.

Animations and Movies

Imaris allows for the simple and straightforward creation of movies from simple rotations to complex animations with objects being turned on and off or cut away to fly-through the objects.

  • Key Frame Animation - The Key Frame Animator allows creation of a movie from key views (frames) in the image. It interpolates frames between the user-defined key frames to create a smooth movie with only a few keystrokes. Simply move the image to the desired position and press the “Add key frame” button to build a movie quickly.
  • Generate Storyboard – The Key Frame Animator stores object visibility states, such as brightness and contrast, color, Clipping Plane position and more, in addition to the camera position and the time point. This feature allows the generation of small storyboards and creation of complex movies.
  • Pre-Defined Rotations – For those that want a simple movie, just click one of the pre-defined movie buttons to make a simple rotation about a given axis.
  • Share Your Results - Create movie files on any platform and easily export these 3D and 4D movies as QuickTime, AVI, MPEG or Flash files with the press of a button. The frame rate and compression settings can be easily controlled.
  • Select movie size - Choose your movie format from a comprehensive list - screen image size to 1080p HD format and more.
  • Z-Movie – Record a simple movie of playing up and down through the different focal planes of your Z stack.
  • T-Movie – Record a simple movie of playing through the different time points of your time lapse image.

Multithreading & Advanced Computer Graphics

The speed and performance of Imaris is enhanced through the use of advanced computer graphics and multiple processors / cores. Using a top-of-the-line computer graphics card allows visualization tasks to be completed at a much faster rate which can be especially convenient for larger datasets. Utilizing multiple processors or multi-core processors can significantly speed calculation times.

  • Multithreading – Imaris is able to utilize multiple cores and / or multiple processors to significantly improve the speed and performance of the software. Most image processing functions and object creation (segmentation) steps are capable of utilizing multiple threads. You can set the number of cores or processors that Imaris can use.
  • High Resolution Rendering - Imaris allows creation of high-resolution images, larger than the resolution of the computer screen for use in publications and poster production.
  • Hardware Driven Computation – Shadow Rendering and most other visualization processes are computed by the graphics processing unit (GPU) to improve the performance of Imaris.
  • Selective Clipping Planes – The Clipping Plane selectively cuts away objects on one side of the plane. It can be freely moved and rotated in the scene and allows you to look inside any object at any angle and any depth.
  • Multiple Light Sources – A Light Source serves to illuminate objects in the viewing area and gives a more 3D appearance through shadows that are cast and reflections on the object for an image presented on a 2D screen. Applying multiple light sources to your image creates spectacular 3D objects because it highlights fine surface details that may otherwise be hidden.
  • 3D Holographic Rendering Modes – Imaris is capable of rendering images on a 2D screen so that they may appear 3D to the human eye. The Red/Cyan Anaglyph mode allows 3D viewing with Red/Cyan glasses. Interleaved or Quad Buffered modes allow for use of the software with 3D shuttered glasses.

Image Editing

One of the key strengths of Imaris is its usability. Automation and hidden image processing intelligence allows users to focus on experiments rather than on the technicalities of the software. However, if more control over the software is needed, Imaris provides the necessary tools to edit datasets manually but effortlessly. The combination of all these tools will result in a dataset that can provide amazing pictures.

  • Basic Editing – Imaris allows the addition or deletion of channels, slices, and/or time points.
  • Re-Sampling In Space And Time – Data sets can easily be re-sampled. Re-sampling in 3D reduces the voxel density in a data set, re-sampling in 4D over time reduces the number of time points. Re-sampling can happen before or after the data set is opened and loaded in the program and therefore speeds up image data processing.
  • Free Rotation tool - If a 3/4D image stack was acquired from a less than optimal point of view (e.g. due to unfortunate embedding and positioning of the sample) it can be arbitrarily rotated in three dimensions. By re-sampling the image along your preferred axis of view it is now possible to access all the hidden information of your specimen’s rendering. This may help to freely reorient your image in 3D so that all images have identical orientation for easier comparison.
  • Crop Images In Space And Time – Cropping the data set in 2, 3 or 4D allows re-sizing of the images down to a region of interest (ROI), making it easier and faster to handle the viewing and storing of the images. Cropping of the dataset has a real-time preview and can be completed either before opening a dataset or once a dataset has been opened.
  • Subregion Processing - By setting a customized subregion Imaris can remain interactive even when working on very large images. Interactively define the subregion in a 3D view and create Spots and Surfaces only within one or more sub ROIs. Once all the correct processing parameters have been determined for the sub region(s), the algorithms can be automatically run on the entire dataset.
  • Volume Painter – Allows drawing disks, spheres, or hollow spheres into the selected image channel, Imaris uses the Volume Painter to manually clear selected areas in the volume image. Additionally, the Volume Painter allows adjustment of the voxel intensities before segmentation is completed with Surfaces, Spots, Cells or Filament Objects.
  • Image Processing Tools - Imaris contains several basic image-processing tools to aid in visualization and image analysis. These tools include 3D Gaussian and Median filters, Baseline and Background Subtraction, and Threshold Cut-off, all which can be used to refine the dataset.

Time

For 4D data, a simple to use time-slider extends all 3D functionality to 3D + time (4D). Imaris memory management and caching mechanisms allow processing large datasets and achieving extraordinary visualization performance. Often images can be rotated in real-time in 3D as they play over time.

  • Loading – Time based images (2D+Time or 3D+time) can be loaded from all native file formats as well as TIFF and BMP images. If time stamp calibration is available with the original image it is utilized. Users have the option to time code non-calibrated images within Imaris.
  • Time-Slider – The Time Slider is visible in all display modes (Slice, Section, Gallery Easy 3D, and Surpass). It allows viewing a particular time point or to automatically play images through time simply by moving the time slider or pressing the play button. The Time Slider uses the calibrated units and shows time data loading progress when opening a time lapse file.
  • Identical Interface - All visualization, image processing, display adjustment, segmentation, and object creation steps can be carried out in the exact same manner on 4D images as they are on 3D images.

Calibration

Imaris always displays the correct aspect ratio of all pixels or voxels (a pixel with depth) in an image regardless of the view. Images are automatically calibrated if calibration information is present in the native file format. Alternatively, the user can calibrate the image by simply entering the size of each voxel in the program.

  • Scale Bar - Imaris includes an automatically adjusting scale bar that is present in the Slice, Section, Gallery and Easy 3D views. This scale bar can be resized and moved interactively based on each user’s needs.
  • Grid – In the Surpass view a grid behind a 3D image can be turned on to provide information about the size of its structures. The properties of the grid can be edited to change color, grid spacing, font, shading, etc.
  • Image Axis - The image axis can also be displayed to simplify orientation of the data set.

General

  • Windows
    • 7, 8 - 64 bit
  • Macintosh OS X
    • OS X 10.7 ("Lion") or later
  • Supported formats
    • Andor: Multi-Tiff (Series) (*.tiff, *.tif)
    • Andor: iQ ImageDisk (*.kinetic)
    • API DeltaVision (*.r3d, *.d3d, *.dv)
    • Biorad MRC 1024, 600 Series (*.pic)
    • Biovision: Ivision (.ipm)
    • Bitplane: Imaris 2.7, Imaris 3, and Imaris 5.5 (*.ims)
    • Bitplane: Imaris Scene File (*.imx)
    • BMP (adjustable file series) (*.bmp)
    • Carl Zeiss Image CZI (*.czi) 
    • Gatan: Digital Micrograph series (*.dm3)
    • Hamamatsu: (Formerly Compix) SimplePCI (*.cxd)
    • Huygens ICS/IDS (*.ics, *.ids)
    • Image Cytometry Standard ICS/IDS (*.ics, *.ids)
    • IMOD binary file (*.imod, *.mod), object scene file
    • Leica Image Format LIF (*.lif)
    • Leica LCS (*.tif, *.tiff, *.lei, *.raw)
    • Leica Series (*.tif, *.tiff, *.inf, *info)
    • Leica TCS-NT (*.tif, *.tiff)
    • MetaSystems MetaViewer (*.imv)
    • MDS Analytical Technologies (Formerly Universal Imaging / Molecular Devices) Metamorph Stack (*.stk)
    • MDS Analytical Technologies (Formerly Universal Imaging / Molecular Devices) Metamorph ND (*.nd)
    • MicroManager file (Image5D)
    • MRC (*.mrc, *.st, *.rec)
    • Nikon ("Huygens compatible") ICS/IDS (*.ics, *.ids)
    • Nikon ND2 (*.ND2)
    • Olympus Cell^R 1.1 (*.tif, *.tiff)
    • Olympus FluoView (*.tif, *.tiff)TIFF
    • Olympus OIB (*.oib)
    • Olympus OIF (*.oif)
    • Olympus Virtual Slide Image VSI (*.vsi)
    • Open Microscopy Environment Tiff (*.tiff, *.tif)
    • Open Microscopy Environment XML (*.ome)
    • OpenLab LIFF (*.liff)
    • OpenLab Raw (*.raw)
    • Perkin Elmer: Ultraview (*.tim, *.zpo)
    • Prairie Technologies: PrairieView (*.xml, *.cfg, *.tif, *.tiff)
    • Scanalytics: IPLAB (*.ipl)
    • SlideBook (.sld)
    • TIFF (adjustable file series) (*.tiff)
    • TILLvisION (*.rbinf)
    • Zeiss Axiovision (*.zvi)
    • Zeiss LSM410, LSM310 (*.tif, *.tiff)
    • Zeiss LSM510, LSM 710 (*.lsm)
  • Image loading properties
    • You are able to open multiple Imaris files by selecting the "Open in new window" command.
    • Automatically extract and read original image data properties (If present in the file)
    • Imaris searches the file header information to extract the maximum metadata fields
    • Image thumbnail preview for data files containing multiple images (LIF, LEI, Andor iQ image disk)
    • All 5D images from the Andor iQ image disk can be read , however additional dimensions are currently not supported, e.g. confocality.
  • Image properties from microscopic files
    • Channel colors or look up tables
    • Emission and / excitation wavelength
    • X, Y, Z Voxel sizes and units
    • Number of time points and time stamps
    • Data type and set name with descriptions
    • Numerical Aperture (NA)
    • Channel name and description
  • Imaris file convertor - Stand alone application the comes free with Imaris.
    • Setup a list of files (any that Imaris can read), and convert all of them into the Imaris 5.5 file format.
    • The tool can also create other file format:
      • RGBA-Tiff (series)(*.tif *.tiff)
      • Tiff (more than 8 bit/Channel series)(*.tif *.tiff)
      • ICS file (*.ics *.ids)
      • Olympus: Virtual Slide Image and cell^R 1.1/standard (*.tif *.tiff)
      • Open Microscopy Environment Xml (*.ome)
      • Open Microscopy Environment Tiff (*.tif *.tiff)
      • BMP (series)(*.bmp)
  • Display
    • Display adjustment
      • Channel Intensity Histogram
      • Blend Opacity
      • Intensity Range
      • Gamma

Data Management – Arena View

  • Organize and manage
    • Full experiments in Assays and Groups
    • All image related resources ((e.g. raw data, segmented results, image analysis protocols) in Groups
    • Vantage (requires ImarisVantage license)
      • Combine dataset into collections to generate Vantage plots from multiple datasets
    • Manage Interface to Batch Processing (requires ImarisBatch license)
      • Manage Batch creation parameters and results
      • Control the Batch processing
    • Build Vantage plots from Batch results (requires ImarisVantage license)
    • Export Statistics belonging to a Collection of datasets into one file (requires MeasurementPro license
  • Search
    • Tag resources
    • Search for tags in the full database or a selected Assays or Groups only
  • Display
    • Gallery of Image Thumbnails with dataset name and icons for dimensions, analysis results (3D view objects) and ImarisBatch processing status (Batch status requires ImarisBatch license)
    • View image related metadata
  • Multi user enabled. Each user sees his data only

Loaded data set editing

  • Visual 3D cropping and time Cropping
  • 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
  • Free rotation for reorientation of specimen in dataset

Visualization - Surpass View

  • Layout
    • Scene Pane – All visualizations are shown including original data and derived / segmented objects
      • Orthogonal or customizable perspective viewing
      • Stereo rendering (red/cyan, interleaved, quad-buffered)
    • Object List – A list of each object shown in the scene pane
      • Objects include: Volumes, Surfaces, Spots, Orthogonal Slices, Oblique slices. Clipping Planes, Light Sources, Frames, , External Objects and Topography representations.
      • Objects requiring a MeasurementPro license: Manual Contour Surfaces, Measurement Points
      • Objects requiring FilamentTracer license: Filaments
      • Add or remove objects from the list view
      • Show or hide any object by simply clicking a checkbox
      • Re-order the items in the list for use in advanced visualization techniques where multiple objects interact
      • Select an object to view the associated properties of the object in the properties window
    • Properties Window - General
      • Shows the current settings specific to each object which can be interactively changed
      • Alter the color properties of the selected object (when applicable)
    • Properties Window – Derived Objects (Surfaces, Spots, Contour Surfaces, and Filaments)
      • Holds the creation wizard when setup of an object is required
      • Allows for inspection of the creation parameters on completed objects and rebuilding of those objects
      • Allows manual editing of the objects
      • Allows for Sorting and Classifying Only when combined with the Imaris MeasurementPro module
      • Allows buttons for custom code to be integrated only with the Imaris XT module
  • Freely zoom, pan or fly through the image , interactively and in real time
  • Combine in the scene view any number of objects (original or derived data)
  • Docking options for Imaris windows and toolbars – e.g. when working with 3D View statistics window, it may be desirable to undock and place the 3D View toolbar on an adjacent screen.
  • Volume Object
    • Automatically displays original data in 3D space
    • Real-time interaction and display
    • Projection Modes
      • Maximum intensity projection (MIP)
      • Alpha blending (Blend) with interactive transparency adjustment
      • Normal Shading – A surface like rendering, where shadows occur away from the light source
      • Shadow Projection – A combination of blending and having a shadow effect
      • Minimum intensity projection
    • Rendering quality can be altered to improve performance on huge datasets or with poor graphics cards
    • Volume Painting / Editing
      • Original data can be altered by adding or removing intensity values from specific locations
      • Choice of disk, sphere, or hollow sphere for editing
      • Works interactively in 3D space
      • Works on a per color channel basis
    • May have lighting effects applied to it
    • May only be created once
  • Surface Object
    • A computer-generated representation of a specified region of interest in the data set
    • Visualized as artificial solid object
    • May have lighting and color properties applied to it
    • Color properties can be selected from a predefined palette or custom created and saved
    • Excellent for segmentation – See Segmentation - Surfaces
    • Excellent for the overlay of original and segmented data
    • Can be visualized as a center point for complex datasets
    • May be created multiple times with different parameters
  • Spots Object
    • Visualized as a sphere with a three dimensional position and time location
    • Can be visualized as only the center point for complex data sets
    • Excellent for modeling point like structures
    • May have lighting and color properties applied to it
    • Excellent for segmentation – See Segmentation - Spots
    • Excellent for the overlay of original and segmented data
    • May be created multiple times with different parameters
  • Light Source Object
    • Produces lighting effects by an artificial light that shines onto the surpass scene
    • Applies to volume, surface, spot, filament and frame objects
    • Interactively positioned in real-time at any angle to the data set
    • Interactively adjusted intensity
    • Positioned in a fixed location or positioned relative to the data set (even as the data is rotated)
    • Excellent for showing surface detail and producing a 3D effect on a 2D screen
    • May be created multiple times with different positions and / or colors
  • Clipping Plane
    • Utilized to cut away data / objects – all objects on one side of the plane are shown and on the other side are hidden
    • Applies to all objects in the object list that are below the clipping plan in the list (providing selective clipping capability)
    • Interactively positioned in real-time at any angle to the data set
    • Cut location can be shown with a plane or hidden for better data viewing
    • Excellent for revealing hidden structures or cutting out complex or noisy area
    • May be created multiple times with different positions
  • Orthogonal (Ortho) slicer
    • View a single slice along the x-y, x-z, or y-z axis
    • Interactively move the slice in real-time
    • View extended focus representing a customizable number of layers
    • Excellent for looking at specific planes along an axis
    • May be created multiple times with different positions
  • 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
    • View extended focus representing a customizable number of layers
    • Excellent for finding data in a plane not aligned with an axis
    • Excellent for finding data in a plane not aligned with an axis
  • Frame
    • Viewed as grid shown behind and on two sides of the data set
    • Utilized to show 3D scale of objects
    • Customizable for spacing, labels, tick marks, line width, shading, shadowing or color
    • May be created multiple times with colors, but will be overlaid
  • External Object
    • Allows import of an external (non-Imaris) object into the surpass scene
    • Objects must be in the *.IV or *.WRL format
    • May be created multiple times with different positions or objects

Image Processing

  • All functions operate on 2D, 3D, and 4D images
  • 3D noise filters (Gaussian, edge preserving, median)
  • Basic and advanced threshold (baseline subtraction, threshold cut-off, background subtraction, connective baseline)
  • Contrast adjustments (linear stretch, gamma correction, inversion, local contrast detection)
  • Channel adjustment and shifting (registration correction)
  • Channel extraction typically from RGB images based on color difference to a reference Voxel
  • Image rotation and flipping
    • Free image rotation (axis and angle)
    • Fixed X, Y, Z flipping
    • Fixed X, Y, Z rotation
  • Custom image processing functions added through the ImarisXT module
  • Fiji/ImageJ - access the plug-in library to run Imaris-compatible plug-ins. Plug-ins include Bio-Formats, Skeletonization, convolution, FFT, various spatial filters, SPIM registration and specialized segmentation options. For detailed description of plug-ins' examples and functionality please refer to: http://rsb.info.nih.gov/ij/plugins/ and http://pacific.mpi-cbg.de/wiki/index.php/Fiji
    • Please note: Imaris Fiji/ImageJ compatible plug-ins are plug-ins that provide image data as a result.

Segmentation - General

  • Segmentation on a per channel basis
  • Automatically works on 2D, 3D or 4D datasets
  • Wizard driven interface to guide users step by step through the segmentation process
  • Ability to perform the segmentation on single or multiple regions of interest (ROI’s)
    • Excellent for large data sets to focus on areas of interest for fast processing
    • Ability to apply set criteria to the entire dataset after ROI processing
  • Ability to perform the segmentation on the entire dataset
  • Intelligently pre-selected (default) settings at each creation wizard step
    • Settings are automatically set on a per image / channel basis
    • Allows for processing large datasets after ROI processing without changing the parameters
  • Manually change pre-set parameters as needed
  • Remember, save and import surfaces, spots, cells and filaments objects creation parameters to use identical settings for analysis of another data set.
  • Ability to Undo last action for Edit, Track Edit and Draw commands - perform multiple undo actions back in sequence history starting with the most recent one and working backwards through the sequence. All actions in the Edit, Edit tracks, and Draw tabs as well as the image processing functions can be undone by selecting Undo command or by pressing Ctrl+Z. The number of any previously applied command that can be Undone/Redone is user defined
  • Filter / Classify segmentation objects as part of the creation process
  • Rebuild the segmentation once completed
    • Ability to change a few parameters once result is seen
    • All other parameters remain as previously set
    • All settings for processing are recorded
  • If image is over time (2D +T, or 3D +T) the resulting segmentation can be tracked with ImarisTrack

Segmentation - Surfaces

  • Segmentation based on an intensity threshold
  • Segmentation based on local contrast
    • Object detection does not depend purely on intensity
    • Excellent for uneven staining or unevenly illuminated fields, bleached or fading samples, and thick specimens
  • Smoothing with a Gaussian filter for noise reduction possible
  • Interactive manual selection of threshold values with real-time visual feedback
  • Split touching objects with region growing
    • Separates objects that other methods would detect as single objects
    • Utilizes an intelligent seeded watershed algorithm
    • Excellent for objects that are close together or where out of focus light overlaps
    • Automatically insert spot objects as seed points
    • Interactively include or exclude seed points with real time visual feedback
    • Result accurately conforms segmented region to objects true shape and size
  • Resulting objects can be filtered as part of the creation process
  • Resulting objects that don’t touch in 3D space can be treated independently
  • Semi-Automatic Surface Creation – Marching Cubes
    • Performed in 3D space in real time on the volume image
    • Performs segmentation only in the bounding box of the cursor
    • Automatically calculates a threshold based on the voxels in the bounding box
    • Excellent for localized segmentation (point and segment)
  • Semi-Automatic Surface Creation – Magic Wand
    • Performed in 3D space in real time on the volume image
    • Reads the intensity value at the cursor location
    • Segments all regions touching the selected voxel that have an intensity at or higher than the selection
    • Ideal for segmentation of discrete but complex objects
  • Manually click in 3D space to remove objects as desired
  • Utilize surface objects to mask the original data
    • Exclude or include original data inside the object
    • Apply mask to any color channel
    • Duplicate masks to other time points
  • Cut single objects apart with a surface scissors as required

Segmentation - Spots

  • Automatic detection of local intensity maxima in 3D
    • Excellent for independently segmenting otherwise touching objects
    • Excellent for objects that are sphere like in shape
    • Excellent for uneven staining or unevenly illuminated fields, bleached or fading samples
    • Excellent for samples with poor signal to noise ratio
    • Excellent for samples with limited Z resolution
  • Option to handle elongation artefacts along the Z axis
  • Interactive inclusion / exclusion of segmented objects with real time visual feedback
  • Region grow to accurately determine the size of each object
  • Manually add or delete spots in 3D space as needed
  • Works on thousands or hundreds of thousands of objects

Interaction and Selection

  • Select individual objects or multiple objects on a single screen in either the visual image view (the scene) or the object list
  • Intelligently select objects in 3D by automatically finding the correct depth location in a single mouse click vie via AutoDepth positioning and selection
  • Snap the 3D cursor to planes, surfaces or centers of objects
  • Manual 3D placement of the cursor for generation of object possible in case of lag of reference voxels or objects
  • 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 to allow object selection from the most complex images
      • Set any object as the center of rotation for the entire image
      • Group objects of interest by dragging them to a group folder in the object list

Visualization - General

  • Multi-resolution rendering to display huge images and keep visualization interactive
  • Smart 3D view caching for fast play back through time
  • Real-time contrast, brightness, and gamma 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 (Time) by moving the time slider
  • Overall Image Display
    • Full Screen Mode – No tool bars
    • 100% Mode – Matches the screen and image resolution (1 pixels per 1 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
      • Inspect individual slices z slices
      • Precise measurements of voxel intensity on a per voxel basis
      • Simply 2D and 3D distance measurements
    • Section view
      • Interactively display slices in x-y, x-z, or y-z at the same time
      • Perform extended focus visualization of a precise number of sections along any axis
      • Render extended focus sections in MIP, Mean or Blend modes
    • Gallery view
      • Overview of all the sections or a selection of sections in the image
      • Display of only selected slices possible
      • Real time zoom and pan of the images in the gallery
    • Easy 3D view
      • Produces a fast maximum intensity (MIP) or blending projection
      • Artificial lighting can be applied for a more 3D look
      • Projection is along the Z axis only

Output

  • Snapshots
    • Produces TIFF image of the image in the viewing window of the program (can be any view)
    • Captures any objects or items in the viewing area including scale bars, time codes, or measurements
    • Captures the image at the resolution shown on the screen, one of many preset values, or any custom resolution
    • Provides off-screen rendering for high resolution high-quality pictures and posters
    • Provides customization of the dots per inch (DPI) of the resulting image
  • Shows preview of result before saving it
  • MovieMaker (Key Frame Animation)
    • Simple and easy to use animation system
    • Create simple preset rotations or complex custom animations and fly-throughs
    • Fast animation definitions using key frames by visually defining “key” positions and adding them
    • Smooth interpolation of camera positions and time points
    • Control for object visibility, color, contrast, brightness, transparency, clipping planes, and slicers
    • Create movies in multiple size formats - from current window size to 1080p HD and beyond
    • AVI, Flash, MPEG1 and 4, QuickTime movie, TIFF series and Window Media output
    • Control for movie length, speed, frames, and compression
  • Dataset file saving as Imaris, OME, Olympus Cell^R, ICS, BMP, TIFF series formats or as movie (AVI, Flash, MPEG1 and 4, QuickTime movie, TIFF series and Window Media Video)
  • Saving of all objects in the object list into IMS (the native Imaris File Format) file to allow continuation of work at a later time
  • Export Surpass objects as VRML or IV files

Tutorial

  • Access tutorial movies from Imaris Help menu to give you a basic introduction to some of Imaris visualization and analytical processes like rendering, tracking and measurements
Learning Center
Webinar Imaris 8.1 - Launch Webinar
Webinar Labelling and Confocal Imaging of Neurons in Thick Invertebrate Tissue Samples
Webinar Imaris 8 Launch Webinar
Webinar Biofilm Formation
Webinar Introduction to Imaris
Webinar Introduction to Imaris - Data Analysis Made Easy
Webinar Live Imaging in Embryonic Zebrafish
Webinar Quantitative single-cell imaging of living pre-implantation embryos
Webinar Cell behaviours during 3D tube formation
Webinar Modelling and Analysis of Collective Cell Migration
Webinar Introduction to Imaris - China
Webinar Introduction to Data Management and Image Analysis using Imaris
Webinar Imaris 8.2 Launch Webinar
Webinar The Search - Cancer
Webinar Imaris for Neuroscientists
Webinar Introduction to Imaris 8.1 - Data Management and Image Analysis
Webinar The Search - Alzheimer’s Disease
Webinar The Search - Alzheimer’s Disease
Webinar The Search - Alzheimer’s Disease
Webinar The Search - Alzheimer’s Disease
Webinar The Search - Alzheimer’s Disease
Webinar Whole Brain Imaging with STP Tomography
Webinar Passive and Whole Body CLARITY for Single Cell Phenotyping
Webinar Passive and Whole Body CLARITY for Single Cell Phenotyping
Webinar Passive and Whole Body CLARITY for Single Cell Phenotyping
Webinar Passive and Whole Body CLARITY for Single Cell Phenotyping
Webinar Passive and Whole Body CLARITY for Single Cell Phenotyping
Webinar Imaris Introduction
Webinar Open spin microscopy and functional imaging in Zebrafish through light sheet microscopy
Webinar Design and Characterization of Functional Biomaterials Made of Natural Building Blocks
Webinar Imaris 7.7 Launch
Webinar Imaris 7.2
Webinar Imaris 7.1
Webinar Imaris in Facilities
Webinar Imaris Contouring V 6.4
Webinar Huge Images & Imaris 6.0
Webinar System Requirements
Webinar Advanced Movies
Webinar Deconvolution
Webinar Imaris Open Launch
Webinar Imaris 7.6 Launch
Webinar Imaris 7.5 Launch
Webinar Visualization and Analysis of Intracellular Dynamics
Webinar Imaris 7.4
Webinar Imaris 6.1
Case StudyVisualizing intracellular molecular interactions during an immune response
Case StudyVolume imaging of Alzheimer’s disease reveals a 3D picture
Case Study24-hour time-lapse imaging of vertebrate embryo morphogenesis
Case Study3D distance calculations for stem cells in bone marrow
Case StudyStudying cell division in 3D tumor models
Case StudyTracking 3D dynamics of individual microtubules in the cell’s mitotic spindle
Case StudyTracking of thousands of neural stem cells with single cell resolution
Case StudyAnalysis of highly dense purkinje cell dendritic spines
Case StudyIntravital imaging of secondary axon death after spinal cord injury
Case Study3D imaging of axons in transparent tissue
Case StudyReliable quantification of dendritic spine density
Case StudyReliable quantification of dendritic spine density
Case StudyReliable quantification of dendritic spine density
Case StudyReliable quantification of dendritic spine density
Case StudyReliable quantification of dendritic spine density
Case Study3D tracking of microglial response to neuroinflammation
Case Study3D tracking of microglial response to neuroinflammation
Case Study3D tracking of microglial response to neuroinflammation
Case Study3D tracking of microglial response to neuroinflammation
Case Study3D tracking of microglial response to neuroinflammation
Case StudyStudying human immune cell interactions in three dimensions
Case StudyHigh-Resolution Imaging in Zebrafish
Case StudyA three-dimensional atlas of the skin’s immune cells
Case StudyViewing microscopic myoanatomy of echinoderes in 3D
Case StudyVisualizing influenza A viral RNA assembly during infection
Case StudyTracking malaria movement in three dimensions
Case StudyMasking method reveals new aspects of neuron morphology
Case Study3D analysis of phase-separated structure of a polymeric membrane
Case StudyTracking changes in asphalt microstructure resulting from traffic
Case StudyTomographic Spectral Imaging, Analysis and Visualization
Case StudyStudying dynamic stem cell interactions in the mouse neocortex
Case StudyA 3-D look at cell division in cancer stem cells
Case StudyStudying vessel morphology and blood flow in the brain’s subependymal zone
Case StudyDynamic imaging of bone marrow mesenchymal stems cells in response to immune challenge
Case StudyStudying cell fate and cellular organization during plant reproduction
Case StudyInvestigating Non-Neovascular Remodeling in the Retina
Case StudyInvestigating Non-Neovascular Remodeling in the Retina
Case StudyInvestigating Non-Neovascular Remodeling in the Retina
Case StudyInvestigating Non-Neovascular Remodeling in the Retina
Case StudyInvestigating Non-Neovascular Remodeling in the Retina
Case Study4D quantitative analyses of virus infection
Case StudyDistinguishing cell types with masks


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