Features

Data Sets

Working with large image data

• smart handling of data sets of almost any size ( >750 Gbyte possible) regardless of main memory (RAM)
• any number of spectral channels
• data sets with up to 6 dimensions (x, y, z, time, spectral channels, scopes)
• Color depth: 8 bit, 16 bit, 32 bit
• merging of multiple data sets in one file (scopes) for multi-well
• linking of any kind of metadata with any kind of data region
• ability to save changes to documents
• Snapshot Management to store different versions in one *. SIS file

arivis Brower- Handling of Datasets: any number of spectral channels

z-Stack: 1,7 GByte in Live-4D (Prof. Matthias Gunzer, Molekulare Immunologie, Uni Magdeburg)

digital Slide: 1,8 GByte (Prof. Dr. Dr. Pahnke, NRL, Uni Rostock)

Personal WebView for collaborative exploration

• Fully integrated sharing feature - no separate server needed!
• Easy sharing of image data over local network
• Present even the largest images in 2D and 3D directly to your team
• Discuss your experiments with your workgroup without the need to copy tons of gigabytes

Snapshot Manager

The arivis imagecore file format provides versioning capabilites that are used for the comfortable UNDO/Redo handling as well as for specifically creating long-lasting versions of your image data within one .SIS file: Snapshots.
A single snapshot stores all your image data, the available metadata and the created annotations. Therefore it can be easily support different filter and analysis experiments.

Save Management

A fully revised save management supports the storage of processed image data. If a document is closed, it is possible to save changes or discard.

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Image Fusion

• Image Fusion of multimodal image data of different pixel size and pixel type (eg. CT/MRI)
• combination of 2D, 3D and 4D image data of different origin

Viewer selection

• several viewers for visualization of 2D, 3D and 4D image data
• overview of the data set (planes, frames, channels) in a Gallery Viewer
• combination and linking of several different viewers also as a split view
• overview of multi-wells in a Well-Plate-Viewer
• Colocalization viewer to represent the spatial dependence of colored structures in multi-channel images.
• Projection Viewer for orthogonal sectional planes, orthogonal projections and free 3D sectional planes
• viewing and editing structure and metadata
• adding, renaming and deleting scopes and channels as well as frames and planes

arivis Browser - Visualization: different views of one data set in a 2 x 2 grid

arivis Browser - Visualization: 2D View of Nanoparticle in HeLaCells with channel and histogram

arivis Browser - Visualization: different views of a CT-data set

Projection Viewer

The Projection Viewer allows you to calculate and export high resolution projections of 3D or 4D image data. In combination with a 4D Viewer you can even define and visualize a freely oriented sectional plane.

Different projection modes are selectable:

• Projection mode allows you to calculate a high resolution projection of a sequence of images along one dimension of your image data (X, Y, Z, time)
• Othoslicer provides controls to calculate one single high resolution slice within your image data along one dimension of your image data (X, Y, Z, time)
• Sectional plane mode allows you to visualize a free projection. In contrast to the Projection or
• Orthoslicer mode you are not restricted to the original orientation of your image data

Use the 4D Viewer's Sectional Plane (new) to interactively define the position and orientation of an oblique slice and immediately calculate a high resolution slice presentation in the Projection Viewer.

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2D, 3D and 4D (3D over time) Visualization

Color Handling

• powerful color management system for mapping intensity values to color values (RGB)
• standard pipeline for each new image stack
• utilization of different gradients (preset or user-defined) for the different spectral channels
• colorbar (linear or logarithmic) for a review of the preset gradients of the individual channels
• application of simple operators such as brightness, contrast or gamma
• auto color range for automated setting of intensity boundaries
• provides easy-to-use tools for color mapping (basic color mapping , advanced color mapping)

Live 4D (3D over time)

• navigating live through very large 3D image data over time without any delay
• 4D visualization of image data as a 3D image and movie over time
• movie player for displaying time lapse experiments
• stereographic 3D imaging also over time

arivis Browser - Live 4D Visualization: 10images/stack; 500Frames; 35h =11GB

arivis Browser - Live 4D Visualization: navigate live through frames

arivis Browser - Live 4D Visualization: navigate in Real-Time and play movie

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3D and 4D Movieexport

• export of complete 3D and 4D data sets or sections as a video stream
• tracking shots through 3D image stack and simultaneous playing of the the series in movie player
• storyboard dor setting key frames
• determine temporal transitions between frames
• set axis of rotation (y, x, z) and duration of the rotation
• select frames for export
• movie preview option
• various resolutions and movie-codec selectable
• movie export as *. avi
• Storyboard und movieexport provides object rotation

arivis Browser - Export: storyboard for movie export

arivis Browser - Live 4D Visualization: rotation settings for movieexport

arivis Browser -Visualization: Fluoreszenz-Image (Pollen) in 3D

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Visualization techniques

• possibility to work with multichannel 2D, 3D, 4D image data
• channel-based mixing of different 3D visualization techniques in one dataset (e.g. Iso Surface and Volume Rendering)
• merging of different 3D visualization techniques in a scene graph
• visualizing intensities and gradients in 2D and 3D

arivis Brower - Visualization technique: channelbased mixing of diff. techniques

arivis Browser -Visualization technique: intensities and gradients in 2D and 3D

arivis Browser -Visualization technique: channel based Rendering in 3D and 4D

• Volume Rendering
  • different rendering modes - Standard, With shading, Maximum Intensity Projection, 3D Texture
  • Maximum Intensity Projection (MIP) for interactive 3D/4D rotation when working on very large image data sets
  • Treshold for segmentation (Basic Slider and Advanced Curve)
• Iso Surface
  • coloring of the surfaces with a predefined color palette or with user-defined palettes
  • simple setting and modifying the colour intensity values
  • selection of different smoothing techniques
• Ortho Slicer
  • movement and simultaneous visualization of a single slice along the x-y, x-z or y-z axis
  • displaying planes along the selected axis
  • repeatable and simultaneous representation displayed in linked views

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Navigation

• Drag & Pan: for a facile navigation through images and time series
• smooth zoom (+/-) and interactive loupe tool
• navigation window to ensure permanent overview of the current position in the frame/plane

arivis Browser - Navigation: loupetool for zoom of ß-Amyloid-Plaques (digital slide courtesy by Prof. Dr. Dr. Pahnke, NRL, University of Rostock)

arivis Browser - Navigation: linked Viewers allows simultaneously view of changes

arivis Browser - Navigation: loupe tool for zoom of Nanoparticle in HeLaCells (Dr. Katrin Claudia Fischer, Freie Universität Berlin)

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Import/Export

Data import

• easy transfer of existing data by drag & drop or an interactive import wizard
• import of data sets from a variety of common image formats such as TIFF, BMP, JPEG, PNG...
• import of biological image data formats such as OME, TIFF, Zeiss LSM, Metamorph STK, ZVI Zeiss, Leica LEI, TILLVisION, Leica LIF, Nikon ND2, VGStudio VOL, Olympus OIF, OIB
• transfer of images and metadata from Till Photonics LiveAcquisition Software
• import of image stacks or time sequences from a video
• acquisition of image data from TWAIN gadgets
• montage of an almost infinite number of single images to an image volume by means of powerful alignment techniques
• Tile Sorter for interactively sort, align and stitch tiled plane

Tile Sorter

Data export

• export to all common image data formats, such as TIFF, BMP, JPG, PNG, …
• creation of screenshots
• copying of selected image regions with flexibly used zoom
• SIS Exporter can generate compressed files (and lossless JPEG)
• very fast JPEG media handler

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Evaluation

Colocalization analysis

The colocalization analysis is used to represent the spatial dependence of colored structures in multi-channel images.
The colocalization is shown in a newly implemented colocalization Viewer, as Colocalization scattergram palette to display intensities of two channels and its statistical analysis. The selected area in the scattergram is shown live in the 2D viewer as an overlay.

RATIO Analysis

The RATIO analysis module allows the ratiometric evaluation of two fluorescence channels or ROIs (region of interests) in multichannel experiments over time.

• simultaneous evaluation of several channels
• algorithm for a background correction
• treshold (optional) for noise reduction
• calculation and storage of ratio images as gray scale image(s)
• measurement and visualization of intensity values over time in virtually unlimited user definable ROIs
• evaluation of changes of medium intensities in ROIs over time in one channel
• minimum and maximum values of ROIs over time
• export of data to Excel file formats or as charts to clipboard

arivis Browser - Evaluation: Ratio Value Chart

arivis Browser - Evaluation: Ratio settings (e.g. channel, min/max)

arivis Browser - Evaluation: Ratio- graph and intensity profile -

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FRET Analysis

The FRET analysis module allows the calculation of FRET values from three-channel FRET experiments.

• selection of channels from drop-down list
• calculation of FRET images per pixel
• Youvan, Gordon and Xia- Algorithmus for FRET and normalized FRET calculation
• XY Offset Alignment for alternation of the original x and y offset values
• Bleed-Through allowing separate entering of bleed-through values for donor and acceptor
• export of calculated values to Excel file format or as charts to clipboard

arivis Browser - Evaluation: FRET Experiment (Dr. Hartmann Harz, BIZ München)

arivis Browser - Evaluation: FRET Bleed Through- type values for donor and acceptor

arivis Browser - Evaluation: FRET Bleed-Through Values (3 scopes shown in one file)

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FRAP Analysis (PlugIn built by TILL Photonics)

The FRAP analysis module allows the evaluation of FRAP data from experiments over time in one or two channels by calculating the average intensity of multiple ROIs.

• ROIs used for the whole cell
• algorithm for background correction with one or multiple ROIs
• correction of photo-bleaching with one or multiple reference ROIs
• evaluation and calculation of mobile and immobile fractions (I1 and I2)
• display of ROI average intensities over time in a graph
• additional graph for normalized values according to the FRAP time
• fitting functions for recovery phase (single and dual exponential)
• export to Excel or to clipboard

Measurements

• simple dynamics for calculation of minimum, maximum and average values of ROIs
• tools for measuring distances and areas of selected objects or selected ROIs
• intensity profile for a precise visualization of intensity values of a channel in 2D and 3D
• evaluation of average intensity changes in ROIs (region of interests) over time in one channel

arivis Browser - Evaluation: tools for measuring distances and areas

arivis Browser - Evaluation: simple dynamics

arivis Browser - Evaluation: Intensity profile of ROI in 3D

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Annotations

• magic Wand tool for an intensity based ROI selection
• various types of annotations for structuring data
• annotations to define ROIs for advanced analysis by setting a rectangle, polyline, ...
• selecting and counting objects with more than 15 different marker annotations
• annotations for different object measurements (length, area)
• text annotations for descriptions and additional information
• annotations for selecting sections and regions for export, analysis, visualization and navigation
• annotation count palette
• annotation properties dialog supports sorting by name

arivis Browser - Annotations: 8-channel: annotated and measured

arivis Browser - Annotationen: Marker for counting objects and ROIs

arivis Browser - Annotationen: Magic Wand for channel based selection

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Analysis

By means of its analysis framework, the arivis Browser provides various possibilities for the quantitative analysis of 2D, 3D and 4D (3D over time) image data.

• MATLAB connection to image processing
• 2D and 3D histograms for random regions of data sets
• filter gallery for an immediate preview after having selected filter methods and operations

Analysis Pipeline

arivis Browser - Analyse Pipeline:
segmentation of objects (Treshold)

The Analysis Pipeline leads the user directly to a result. Image and analysis operations can be individually selected and gradually performed. Already during the gradual analysis, the immediate visualization and the analysis report allow an evaluation and correction of selected parameters. Optionally, the analysis can be carried out on the entire data volume, on selected planes/ frames or on separate image regions.
The analysis result is offered as a report and can be exported.
For visualization and further processing, all features of the arivis Browser are available.

• voxel technique for image processing and image editing
• combination of different selections and filter methods (soft focus, noise reduction, edge enhancement, etc.)
• different methods for segmentation: Threshold, Dual-Threshold, Automatic Threshold (Otsu)
• segmentation, counting and measurement of 2D, 3D and 4D objects
• tracking objects in 3D and 4D (3D over time)
• filter modus for different volume attributes: measurement, counting, etc., of length, surface, etc.
• analysis, visualization, and export of analysis reports (e.g. as *.xls)

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4D Object Tracking (Preview) see also: USE CASE: TRACKING OBJECTS

Object tracking and analysis of cell movement are fields of high interest for neuroscientists, evolutionary biologists, and immunologists. In order to visualize and analyze cell movements, an image acquisition over time is required.

The tracking module of the arivis Browser visualizes, tags and reconstructs object movements and provides the measured parameters in a report ready to be exported.

• tracking of segmented 4D objects (3D over time)
• presentation in 2D, 3D or 4D viewer possible
• identification of objects of the same track
• combination of objects of the same track
• tracking and visualization of the object position over time
• algorithms in order to carry out track measurements, such as: duration, velocity, length, direction

arivis Browser - Analysis Pipeline: segmentation of objects over time

arivis Browser - Analyse Pipeline: Tracking of objects over time

arivis Browser - Analysis Pipeline: Analysis with filtered volume attributes

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Automation

• recording and playing macros
• writing macros by the built in Python Scripting
• implementation of special Plugin-modules freely provided by the API (SDK)
• user-defined keyboard shortcuts

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