Features

arivis Vision4D: 4D Viewer fly-through mode

arivis Vision4D provides smart handling of multi-dimensional data sets of almost any size together with fast and interactive 3D/4D rendering and visualization even on standard desktops and laptops with 3D graphics support. Tools for image import and handling, data pre-processing, fast 2D/3D and 4D visualization, measurement, annotation and presentation are in the 4D Base Package and effective on images up to several TB.

Import & Data Handling

  • Easy drag & drop import of multi-dimensional and multi-channel data sets
  • Data sets up to 6 dimensions (x, y, z, time, spectral channels, scopes)
  • Color depth: 8 bit, 16 bit, 32 bit float
  • Media reader for a variety of biological data formats included
  • Stitching & Alignment with the Tile Sorter
  • Restore Point Manager
  • Audit Trail
  • Reliable Undo / Redo

Visualization

  • Specialized viewers for 2D or 3D/4D image data
  • Quick navigation: drag & pan, scroll, flip through frame/plane, smooth zoom
  • Fast and interactive 3D/4D rendering
  • Interactive “fly-through” mode that enables exploration inside the image
  • Combination of multiple Clipping Planes at different angles and time points
  • 4D Surfaces: create, export & import 4D objects based on Intensity threshold
  • Gallery Viewer
  • 4D Bookmarks: record, save, restore and share interesting views and scene settings
  • Info Viewer to view and edit data structure and metadata
  • Split & link multiple different viewers (e.g. 4D Viewer + Projection View)
  • Projection Viewer to calculate and export high resolution projections of 3D or 4D image data
  • Powerful color management system for mapping intensity values to color values (RGB)
  • Interactive Color Curve, custom gradient editor & presets
  • Auto Color Range
  • Color Bar (linear or logarithmic) for a review and fast modification of the color mapping of the individual channels​
  • Lighting and Projection settings including projection and stereoscopic rendering
  • Movie player for running time lapse series in 2D or 3D
arivis Vision4D: 4D Viewer fly-through mode
arivis Vision4D: extract geometry objects
arivis Vision4D: combination of multiple clipping planes
 

Data pre-processing

  • Transformation and resampling of images or regions of interest including: e.g. cropping, flipping, rotation, change of bit depth as well as dimensions 
  • Drift correction to a user-selected reference track for more accurate quantitative analysis of drifting time lapse data 
  • Bleach correction for better visualization and quantification of dynamic time lapse experiments 

Evaluate & Measure

  • 2D and 3D histograms
  • Filter Gallery: quick preview and apply pixel filter for image enhancements
  • Create annotation (segment, rectangle, polyline, ellipse, marker, …) manually or with the Magic Wand tool
  • Manual functions to split and/or merge segments in the 4D Viewer
  • 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

Presentation & Sharing

  • Export image channel data as TIFF or composed RGB image as TIFF, BMP, JPG, PNG, …
  • Save viewer content as a screenshot or copy selected image regions with flexible zoom
  • Easy design and export of 3D/4D High Resolution Movies to produce complex movie sequences in 3D (or 3D time series) using the StoryBoard at different resolutions and movie-codecs (e.g. AVI, MP4 …)
  • Team collaboration: show large 2D/3D images to your workgroup with the Personal WebView
  • Burn in annotations, time stamp or navigation position (frame/plane/channel) during export
  • Channel split movie export

Automation & Integration

  • Built in Python Scripting
  • Modular system - expandable with plug-ins in every part, free Plug-in SDK!
  • Documented file format (arivis ImageCore), integration software libraries available

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Additional modules for 2D and 3D + time analysis

A strength of arivis Vision4D is its capability to segment and track cells (ROI) in data sets composed of even hundreds of time frames. Therefore arivis Vision4D provides with the Analysis Pipeline a robust and fast tool for processing of image data gained from long-term timelapse experiments.

arivis Vision4D Analysis_segment 3d objects over time

A Segment Tracker operator allows to track segmented objects at different timepoints within your image series using the Analysis Pipeline. After the process of detecting, filtering and generating segments the Segment Tracker operator will try to find the same object across multiple timepoints and connect segments representing that object to a track.

arivis Vision4D: Analysis Pipeline_join Tracks

The Batch Analysis Module is used for unattended execution of a pre-configured arivis Analysis Pipeline on a series of images, on multiple documents, scopes, or regions. No programming skills are needed. The analysis workflow can be setup using the flexible Analysis Pipeline with easy access on operators and several filters and segmenter functions.

arivis Vision4D: Batch Analysis

The Colocalization Palette in arivis Vision4D enables you to analyze the colocalization of voxel intensities in different channels of your image data and provides interactive visualization in the 2D Viewer. Among others, Pearson's correlation coefficient and Manders split coefficients are two of many colocalization coefficients to express the intensity correlation of colocalizing objects in each component of a dual-color image. These coefficients measure the amount or degree of colocalization, or rather correlation and co-occurrence respectively. 

arivis Vision4D: Colocaliaztion

The Advanced Dynamics Package includes both the moduls to analyse Ratio and FRET. Ratio Analysis allows a ratiometric analysis of two fluorescence channels or regions of interest (ROIs) in multi-channel experiments over time.The FRET analysis method is applied to describe relations between and within biomolecules, so that you can attain quantitative, temporal, and spatial information about their relation and interaction.

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