The fastest and intuitive 2D/3D/4D imaging solution for data of nearly unlimited size. Features & Modules arivis Vision4D Version 2.10.

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1 we are ready for terabyte images The fastest and intuitive 2D/3D/4D imaging solution for data of nearly unlimited size. Features & Modules arivis Vision4D Version Data Handling nearly unlimited size regardless of main memory (RAM) up to 6 dimensions (x, y, z, time, spectral channels, scopes) color depth: 8 bit, 16 bit, 32 bit float optimized storage file format (*.sis) - allows to open or close the data very quickly (independent from size) possibility to store multiple image sets as individual scopes in one file (e.g. for related wells or colocalization results) Restore Points allow to store different versions in one file reliable Undo / Redo - discard or save any changes on closing the data set Audit Trail - logbook for dataset modifications Import easy drag & drop import of multi-dimensional and multi-channel data sets interactive import wizard if ambiguity powerful tools for sorting multiple input files and define dimension order (if necessary) import of common image formats (e.g. TIFF, BMP, JPEG, PNG ) media reader for a variety of biological data formats included (e.g. Zeiss ZVI, Zeiss CZI, Zeiss LSM, Imaris IMS, OME TIFF, Fiji/ImageJ TIFF, Metamorph STK, Leica LEI, Leica LIF, Hamamatsu NDPI & VMS, TillVision, Nikon ND2, VGStudio VOL, Olympus OIF, Olympus OIB, Dicom, ICS, Mirax Slides, DeltaVision DV, NIfTI, AmiraMesh AM ) support for mosaic or multi scene files (e.g. Zeiss CZI or Leica LIF) interactive alignment of single image tiles to a large plane or an image volume (Tile Sorter) with optional blending between overlapping regions import & stitching of aligned tiles from TrakEM2 projects acquisition of image data from TWAIN devices Hardware Control direct acquisition from imaging devices (camera + motor stage) - possible on request

2 Viewers specialized viewers for fast visualization of 2D or 3D/4D image data Gallery Viewer: overview of content of the frames and planes of a data set Well-Plate Viewer: overview of multi-wells files Projection Viewer: for orthogonal sectional planes, orthogonal projections and oblique slices (3D sectional plane) Info Viewer: view and edit data structure and metadata arrange multiple different viewers as a split view link viewers to navigate synchronously Channel Split view workspace editor: define and switch between different viewer setups 2D Viewer quick navigation: drag & pan, scroll, flip through frame/plane smooth zoom tools ColorBar (linear or logarithmic) for a review and fast modification of the color mapping of the individual channels interactive loupe tool Navigator palette for an overview of the current frame/plane position in the data Movie player for running time lapse series Filter Gallery: quick preview and apply pixel filter for image enhancements Color Handling powerful color management system for mapping intensity values to color values (RGB) apply different gradients (presets or user-defined) for the individual spectral channels interactive Color Curve to draw RGB components of gradients custom gradient editor & presets adjustment of brightness, contrast or gamma Auto Color Range for detecting the used intensity range Projection Viewer calculate and export high resolution projections of 3D or 4D image data Projection mode: calculate a high resolution projection of a sequence of images along one dimension of your image data (X, Y, Z, time) Othoslicer mode: calculate one single high resolution slice within your image data along one dimension of your image data Sectional plane mode: calculate a projection at an oblique slice. 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 interactive Sectional Plane to define the position and orientation of an oblique slice to use for a projection in the Projection Viewer save the projection result to a new multi frame or multi plane stack ore scope

3 4D Viewer fast and interactive 3D rendering even on standard PCs and laptops with 3D graphics support navigating live through very large 4D image data (time series of 3D stacks) with ease different visualization modes: Volume Rending, Iso Surface, Ortho Slicer assign visualization mode to each channel independently volume rendering as shaded, flat or Maximum Intensity Projection (MIP) simple threshold range slider for visible intensities advanced threshold curve to define complex intensity visibility and opacity custom threshold curve presets apply special color preset (e.g. rainbow mapped to the z axis) for rendering adjustable quality setup to improve interactivity even on low end hardware support for stereographic 3D/4D (Anaglyph, Tridelity, Side-by-Side, Top-Bottom) native high resolution rendering of 3D volumes for publications (optional as stereographic or MIP image) Volume Clipping with live preview by a region of interest (ROI) by the outline of an annotation (e.g. an extruded polyline) at the Sectional Plane optional inverted Storyboard: quick creation of complex movie sequences in 3D (or 3D time series) measure box orientation cross Presentation & Sharing export image channel data as TIFF export composed RGB image as TIFF, BMP, JPG, PNG, save viewer content as screenshot copy of selected image regions with flexible zoom export data as compressed SIS file save time series as a movie (e.g. AVI, MP4 ) channel split movie export burn in annotations, time stamp or navigation position (frame/plane/channel) during export Storyboard powerful tool to arrange complex movies in 4D add the current 3D view as keyframe interpolates the parameters between two keyframes (including rotation, time point and opacity of the dataset) adjustable temporal transitions between keyframes use keyframe sequence templates to quickly add standard rotations or defined time point sequences live preview of the resulting movie movie export with different resolutions and movie-codecs (e.g. AVI, MP4 ) optional high resolution rendering for movie export

4 Personal WebView team collaboration: show large 2D/3D images to your workgroup with the Personal WebView no separate server required - it s integrated in the arivis Vision4D application no special web browser plugins (like Java or Flash) or other proprietary software needed no need to preprocess or exporting the data for the web allows to present even the largest images directly to your team right after acquisition and to discuss them without having to copy tons of gigabytes beforehand 3D volume rendering in a normal web browser using WebGL live update: any modification on the image data in the arivis Vision4D application is instantly represented in any connected web browser client and hence visible for any user having access to the shared data see what your colleague see: a remote user can follow the navigation of the user currently sharing the data and see the same region (frame, plane, zoom, view area) inside the dataset fully integrated sharing feature - no separate server needed designed for Intranet use Measurements 2D and 3D histograms 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 Colocalization Colocalization scattergram show selected area in the scattergram as overlay in the 2D view statistical analysis export coloc images, coloc statistics or scattergram Advanced Dynamics Ratio ratiometric evaluation of two fluorescence channels or ROIs (region of interests) in multichannel experiments over time background correction noise reduction treshold calculate ratio images charting export of result data to Excel file formats or as charts to clipboard Advanced Dynamics FRET calculation of FRET values from three-channel FRET experiments Youvan, Gordon and Xia- Algorithmus normalized FRET calculation XY Offset Alignment Bleed-Through charting export of calculated values to Excel file format or as charts to clipboard

5 Annotations create annotation (rectangle, polyline, ellipse, marker, ) manually with the Annotation Tools Magic Wand tool for an intensity based ROI selection or annotation creation use annotations to define ROIs (e.g. for volume clipping, export of regions or analysis) count objects with more than 15 different marker annotations text annotations for descriptions and additional information Annotation Properties dialog to sort or modify annotations Filter Gallery quick preview and apply pixel filter for image enhancements Background Filters (removing unwanted background information) (De)Convolution Filters Edge Detection Filters Intensity Filters (transforming and re-scaling the intensity values) Morphology Filters Sharpening & Smoothing Filters Analysis Pipeline Analysis define your analysis workflow by adding image and analysis operators like Voxel Operations, Segmentation, Segment Operations or Track Operations Analysis operations can be individually parametrized and performed step-by-step - even backwards Analysis immediate result visualization and a live analysis report allow an evaluation and correction of parameters during the gradual analysis Analysis the Analysis Pipeline can run on the entire data volume, on selected planes/frames or on specified image regions (ROIs) Analysis the analysis result report can be exported for further processing (e.g. as Excel *.xls or *.csv) Analysis create, export, import or switch between multiple Analysis Pipelines Analysis Voxel Operations for image enhancements and image editing combine different operators and filter methods (noise reduction, blur filters, contour filter, edge enhancement, etc.) Analysis Segmentation Operators for 2D or 3D objects Intensity Threshold RGB Threshold Automatic Threshold (Otsu, Huang, Li, Yen) Analysis Segment Attribute Filter (segment attributes like volume, projected area, size, min, max, mean, roundness, center of mass ) Analysis Segment Distance Filter Analysis Touching Edge Filter Tracking Particle Tracker (brown motion or linear regression) - tags and reconstructs object movements Tracking Track Attribute Filter (track attributes like length, speed, displacement, straightness )

6 Automation & Integration user-defined keyboard shortcuts built in Python Scripting Python scripting support for analysis and most components Script Editor record and play script macros modular system - expandable with plug-ins in every part free Plug-in SDK documented file format (arivis ImageCore), integration software libraries available Paid modules which are not included in the arivis Vision4D Base Package: Analysis Tracking Advanced Dynamics Colocalization Hardware Control arivis AG Business Unit arivis Vision Kroepeliner Strasse Rostock, Germany Phone: +49 (381) Fax: +49 (381) info@arivis.com