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Imaris 3D/4D visualization and analysis

Imaris ( Bitplane ) 是即時定量三維/四維/多維圖像進行視覺化和定量分析的圖像工作站,20 多年來,專注於多維圖像的立體展示和定量分析,堅持不斷創新和完美多維成像的信念,形成了獨特的產品線,為高端顯微圖像使用者提供多維圖像顯示、處理和資料分析系統,是多維圖像領域的黃金標準。






Imaris 始於1993 年的尖端3D/4D/多維圖像渲染及交互分析技術

Imaris Bitplane 公司出品的軟體核心模組,它具備展示、分離、分析及演繹等所有3D/4D 顯微圖像渲染所必須的功能, 具有快速,精准及易於使用的特點,因此對於三/四維多通道 圖像的渲染, 無論是幾兆的小檔,或是幾十GB 的超大圖像,Imaris 都能夠輕鬆勝任。


Imaris 是生命科學領域裡最領先的圖像分析軟體

  • 作為 Imaris 軟體家族的核心模組,Imaris是顯微鏡圖像快速交互展示的基本工具。

  • . 可直接讀取30多種格式的檔,幾乎涵蓋了所有顯微鏡廠家的圖像格式。

  • . 輕鬆處理50 GB 甚至更大的3D/4D文件

  • . 提供Slice, Section, Gallery 等觀察模式,並提供MIP 投影和混合投影模式。

  • . Supass 觀察方式下,各種交互工具結合展示(Volume rendering, iso-surface rendering, clipping planes, spots,slices

  • . 採取易於操作的關鍵幀(key-frame)工具創建內容豐富的電影。

  • . 通過多種分離工具,自動識別並分離數以千計的物體。

  • . 通過多個CPUGPU,及多解析度渲染模式提高Imaris 的分析能力,提高渲染速度 Bitplane 的專利觀察模式 InMotion 使3D 空間中物體的選擇及操作變得非常容易。








General

Operating systems and requirements

  • Windows

- XP, Vista, 7 - 32 bit
- XP, Vista, 7 - 64 bit

  • Macintosh OS X

- OS X 10.6 ("Snow Leopard") or later
- Intel CPU

  • 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)
- 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)
- 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

 

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 & 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)

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

 

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)
  • New docking options for Imaris windows and toolbars - when working with Surpass statistics window, it may be desirable to undock and place the Surpass 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
- May be created multiple times with different positions

  • 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)
  • Double threshold - you can choose two filter values, a Lower and a Higher filter value to separate the data into three regions: above the higher value, below the lower value, and the region in between. Only those objects with qualities inside the defined interval will be considered for visualization.
  • Contrast adjustments (linear stretch, gamma correction, inversion, local contrast detection)
  • Channel adjustment and shifting (registration correction)
  • 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

  • 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 listt
  • Intelligently select objects in 3D by automatically finding the correct depth location in a single mouse click vie via AutoDepth positioning and selection
  • 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

- 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

  • QuickTime VR of any or all objects in the Surpass view for interactive movies (Mac or 32bit Windows Only)
  • 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

  • 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

 

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








(1) 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.



(2) 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 on an intensity value on a per channel basis. Selection of the 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 section of objects where the overall intensity many 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 process 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 can be colored any desired color and given visualization properties for shininess and transparency. Visualization color properties can be selected from a predefined color palette or can be custom designed and saved for future use.




(3) Spots, Segmentation and Interaction

The “Spot Object” is available to model point-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 “Spots Object” is that local maxima can be identified and images with 10’s or 100’s of thousands of objects can be individually identified quickly.

  • Spots – Like the “Surface Object” the “Spots Object” is an artificial object allowing the comparison between the original data and what has been segmented. Like the surface object, the spots 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, 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 or double 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 process 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.



(4) Interactive, Intuitive; Navigation and Selection


  • Advanced On-Line Interaction With The Object – Rotating, zooming in and out of the object and flying 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 - The “Object Filtering” is incorporated into the creation process of surfaces and spots enabling the composition of filters consisting of several criteria and interactive visual feedback on parameter selection.




 

(5) 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 or when using a 32 bit operating system. 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.


(6) 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 and fly through’s being performed.

  • Key Frame Animation - The “Key Frame Animator” allows creation of a movie from key views (key frames) in the image. It interpolates frames between the user-defined views to create a smooth movie with only a few keystrokes. Simply move the image to the desired position and press the add 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 a 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 - from screen image size to 1080p HD format and more.

  • QuickTime-VR Movie – Record a QuickTime-VR movie of anything that is displayed in the 3D view of Imaris. A QuickTime-VR allows the 3D interactive rotation of the resulting image by anyone who has QuickTime outside of Imaris, allowing easy collaboration with other researchers.

  • Z-Movie – Record a simple movie of playing up and down through the different focal planes of your Z stack.



(7) 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 “Oblique Slicer” 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 rending 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 Quard Buffered modes allow for use of the software with 3D shuttered glasses.



(8) 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, which take a matter of seconds to use, 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 total reduces the number of time points. Resampling can happen before the data set is opened or once the dataset is already open in the program and therefore speeds up image data processing.

  • Free Rotation tool - If your 3/4D image stack was acquired from a less then optimal point of view, for example due to unfortunate embedding and positioning of the sample, it can now be arbitrarily rotated in three dimensions. By resampling 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 you freely reorient your sample in 3D so that all your samples have identical orientation when it comes to comparing various samples between different experiments.

  • 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. The total number of time points can be reduced at the beginning or end of the series of images. Cropping of the dataset has a real-time preview and can be completed both 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 – 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, or Filament Objects.

  • Image Processing Tools - Imaris contains several basic image-processing tools to aid in basic 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.



(9) 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 of a particular time point or to automatically play images through time simply by moving the time slider or pressing the play button

  • 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.



(11) 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 users 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.

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