Archive

Summary of changes in arivis Vision4D 4.0, released 30 September 2022.

New & Noteworthy:

• New Automatic Neuron Tracing Module: automatic detection, interactive editing, visualization and features of traces in neuron imaging
• Much cleaner and simplified Object Style UI
• Import Perkin Elmer Operetta and Columbus datasets

Automatic Tracing workflow, optimized for neurons:

• New: introducing a new object type "Trace"
• New: show traces as cones or skeleton in 2D and 3D
• New: automatic tracing analysis operations with two powerful algorithms
• New: neuron tracing starting with a segment as cell body (or without)
• New: manual trace editing with the Trace Tool
• New: ability to manually split, merge, refine, or simplify trace sections within the Trace Tool
• New: interactive Draw mode to add missing sections or start from scratch (or start from a segment as cell body)
• New: action to split trace components (neurites, cell body) apart

Analysis:

• New: Tracking operation now saves the center calculation method used
• New: tracks are correctly retained even if their segments have been deleted
• New: track features are computed based on the stored center calculation
• New: Distances operation calculates statistics for the closest n objects
• New: Background Correction operation supports different methods now (including morphology)
• New: Analysis operations now create object styles to color results
• New: operation categories "Use segments" and "Use track & groups" are now combined as "Use objects"
• improved: region growing results contain the complete geometry of seeds now
• improved: performance improvements for feature calculations for tracks and tracked objects
• improved: better support for scaled analysis of very large planes
• improved: handling of large ML trainings
• improved: allow to choose target directory for extracting zpipeline packages
• improved: do not show sample pipelines that use operations not covered by the current license
• fix: missing configure output menu entry

Object Styles:

• New: simplified style rule UI
• New: each tag has a single style rule now
• New: ability to change the order of processing the style definitions by drag & drop
• New: simplified minimum set of style properties
• New: create styles with specific style properties for object types tracks and traces
• improved: 2D and 3D style settings have been combined for ease of use
• improved: proper Apply button to save the settings but keep the styles dialog open

Data & Import:

• New: media handler for reading Perkin Elmer Operetta and Columbus datasets
• New: wellplate import scenario
• New: the offset of an image set is displayed more prominently in the Info Viewer
• New: ability to delete all objects of several image sets
• improved: import the names of the channels of an OME TIFF
• improved: export OME TIFF with a newer OME schema (June 2016, version 2)
• fix: sort order for the well field in the Navigator panel

Scripting:

• new: scripting support for the new trace objects
• new: scripting support for the 4D Viewer Storyboard
• improved: 4D Viewer scripting capabilities

General:

• New: remember movie export settings
• New: allow to open the License Tool directly in case the maintenance has expired
• improved: visibility of the reason for a deactivated license (e.g. cloned)
• improved: updated included Sentinel driver to version 8.4
• various bug fixes and stability improvements

Summary of changes in arivis Vision4D 3.6.2, released 13 June 2022.

This version contains various small fixes and performance improvements:

• Improved stability when performing Deep Learning inference on multiple CPU cores
• Improved Aperio SVS file import

Full Changelog:

Analysis:

• fix: prevent all possible out-of-memory problems in the Deep Learning Segmenter operation

Misc:

• fix: potential problem with the Aperio SVS import

Summary of changes in arivis Vision4D 3.6.1, released 20 May 2022.

This version contains various small fixes and performance improvements:

• Improved handling of Machine Learning and Deep Learning analysis pipelines
• Improved speed and stability of Deep Learning inference
• Several bug fixes for Analysis Pipeline issues
• Improved quality of VisionHub interface dialogs
• Bug Fixes for ZEN bridge

Full Changelog:

Analysis:

• new: share analysis pipelines with additional files (e.g. Python scripts or Deep Learning models) as *.zpipeline packages
• new: allow upload of *.zpipeline packages to arivis VisionHub
• new: exported analysis pipelines (without additional files) now have the *.pipeline extension
• fix: ensure stored object features will be shown after opening a dataset on a different computer
• fix: potential problems when upgrading older analysis pipelines containing a Blob Finder or a Tracking operation
• fix: prevent possible out of memory problems in the Deep Learning Segmenter operation
• fix: enable *.czseg as valid extension for DL models
• fix: clearer error messages for the Seeded Region Growing operation
• fix: pipeline export dialog memorize last settings better

Misc:

• new: using Microsoft Edge WebView2 as base control for web content
• improved: surface quality for flat datasets
• fix: apply ZEN intensity mapping correctly when image is transferred via bridge to Vision4D
• fix: correctly transfer isosurface visibility and clipping between ZEN and Vision4D
• fix: ensure that a file is closed cleanly even if the process of opening it is aborted

Summary of changes in arivis Vision4D 3.5.1 which was released publicly on 11th Nov 2021.

Analysis:

• Improved: error handling for missing input channels
• New: ability to match missing input channels
• New: more accurate mesh-based calculation methods for surface area and sphericity (using Marching Cubes)
• New: more accurate mesh-based calculation methods for projected area, roundness, and circumference (using Marching Squares)
• New: more prominent Add Pipeline button if there are no pipelines in the document so far
• Fix: preview of analysis operations (e.g. Blob Finder) if the viewer is zoomed out much
• Fix: avoid a potential crash with an empty Compartments analysis operation
• Fix: minor UI glitches in the Compartments' input controls
• Fix: coloring of the output of the Compartments operation
• Fix: potential crash with Configure Output Channels
• Fix: problem on reopening a pipeline with Object Math in 'Merge' mode
• Fix: potential crash with Region Growing's output color configuration
• Fix: avoid error in the Region Growing operation if used with a large number of input objects
• Fix: problem with the labeled image export operation
• Fix: prevent an unwanted change of the current plane on undo of the Input ROI operation
• Fix: incorrect preview for the Enhancement Filter operation
• Fix: prevent problems in the Intensity Profile while modifying channels with a script

Machine Learning:

• Fix: delay on rename a ML training (objects)
• Fix: selection behavior in the ML Trainer (Objects)
• Improved: error indicators in the ML Trainer (Objects)
• Improved: don't collapse classes on switching image set in the ML Trainer (Objects)
• Improved: ML Trainer (Image) together with object styles
• Improved: ML Trainer (Objects) preview together with object styles
• Fix: unexpected stuck with the object classification run
• Fix: avoid problems with parallel running preview operations in the ML Trainer (Objects)
• Improved: tag handling on re-run of the object classification (from trainer panel)
• Fix: more robust test for ML hardware acceleration capabilities
• Fix: no results if running a ML Segmenter operation using 3D features

Objects:

• Improved: better rounding when calculating feature range for object coloring
• Fix: chart updates object colors after style changes immediately
• Fix: problem if there are more than 999 tags
• Fix: more reliable tag selection in the remove tags dialog

4D Viewer & Storyboard:

• Fix: more reliably finish the preview mode after using the storyboard
• Improved: clipping planes in storyboard movie exports
• Fix: legend more reliable
• Fix: track children visibility in combination with master details view
• Fix: potential missing surfaces in storyboard exports
• Fix: under rare conditions objects were not clipped in storyboard movie exports

Import & Data Handling:

• Fix: broken Luxendo Big Data Viewer import
• Fix: better distinction of mosaic and channel-stitching in LaVision OME tiffs
• New: added GZIp preference switch to the Volume Fusion dialog (for new file results)
• Improved: order of tiles imported from a CZI
• Improved: wording for edit support for tiles in manual mode of the Tile Sorter
• Improved: avoid endless metadata entries in the command history if importing tiled data
• Fix: prevent a potential crash in the Save Image to VisionHub dialog

General:

• Improved: allow object classification with launcher configurations
• Improved: a bunch of minor fixes in the help content
• Fix: wrong GPU RAM display in the System Check tool
• Additional minor fixes

Welcome to the arivis Vision4D 3.3 Release Notes - Version Date: July 7, 2020. Please have a look at the Overview of arivis Vision4D Release notes for features we released in prior versions.

New & Noteworthy

• new: dynamic scalebar in the 4D Viewer
• new: scalebar appearance can be customized
• new: transparency render mode in the 4D Viewer

Object Tools

• improved: interpolation of complex shapes in the Draw Objects tool
• improved: Magic Wand preview in the 4D Viewer
• fix: prevent Magic Wand to create non-touching geometries
• fix: improved Split Tool behavior while using Z-Scaling in the 4D Viewer
• fix: potential problem of the Place Object Tool in the 4D Viewer
• fix: proper tag after using the Split Tool

Analysis

• improved: decimal separator handling in some analysis operations
• improved: speedup for geometry validation (e.g. in the Merge operation)
• improved: sort order by color in the objects table
• improved: border calculations for tiled voxel operations
• fix: change color in the Compartments operation
• fix: potential crash with the Background Correction operation
• fix: save Allow Holes parameter for region growing operations
• fix: problems with imported Ilastik trainings
• fix: ML filter operation saves/loads channel selection correctly

Import & Data Handling

• new: support for VGL import
• improved: support for larger translations in the Volume Fusion
• fix: potential problem with importing very large Imaris IMS files
• fix: pixel size and time stamps for ZVI files
• fix: prevent accidental rounding of the pixel size

General

• new: search in the Help app
• improved: Vision4D launcher
• improved: ZEN integration: better channel color support
• improved: error handling in the arivis License Tool
• fix: possible crash on closing documents

Welcome to the arivis Vision4D 3.2 Release Notes - Version Date: 24 April, 2020 -

With a new clean Analysis Pipeline user interface users have a good overview over their analysis pipeline at any time. Paired with several improvements to existing Operations and the addition of completely new Operations, e.g. Seeded Region Growing Operation, users now have the tools to segment any object of any shape. Scaling via headless operation is also possible. Now included is a set of new Sample Pipelines for common analysis tasks and detailed descriptions for an easy start.

Machine Learning Improvements

• Work with colors
• Machine Learning can now be trained on separate channels or for channel combinations. This allows color mixtures with co-labelling to be detected and quantified.
• Import trained ilp files
• We now support the import of pixel class ilastik ilp files, including 3D object features and color information.
• Reuse training for several files
• All training sets can be applied on other image sets which were not used for training one by one or in Batch Analysis.

New Analysis Operations

Flexible Seeded Region Growing

• Use information from different channels for better results
• The Seeded Region Growing Operation uses two different channels to achieve more precise segmentation results. In a simple two-step approach, you can choose one channel for seeding and another one for growing. You can easily segment whole cell bodies based on positive nuclear staining to easily separate close cells.
• New Watershed Operation for easy detection of non-roundish cells
• The Blob Finder has a brother! This Watershed splits objects of any shape.
• Combine Region Growing with Blob Finder or Watershed & VR
• Create great results using any segmenter for seeding, using these as a starting point for Region Growing. Also, objects added into the data set via Virtual Reality can be used for Region Growing.
• Easy splitting within the pipeline
• Use the new Splitting Operation as a modifier of segmentation objects to automatically split them in a pipeline run.

See Overview for the different approaches to cover almost all possible segmentation tasks combining these tools efficiently. Watch Tutorials for more details on how to get executional segmentations results also for touching cells.

Analysis and Batch Analysis Improvements

Distances: centroid to surface measurements

• Tune your Distance Measurements
• Object distances can now be measured by surface-surface, centroid-centroid or surface-centroid basis. This allows for a custom selection of accuracy versus speed. If the particles to be measured against a big surface are small and spot-like, you can choose surface-centroid mode for high speed. In contrast, detail measurements with surface-surface distances give accurate distance measures of surfaces of larger objects.
• Get your Distance Measurements faster
• Several improvements in this Operation boosted speed for all measurement types.
• Combine distances with Tracking and classification easily
• The Distance Measurement Operation is an integral part of the arivis Analysis Pipeline and can be combined with other Operations such as object filtering or tracking, and directly group objects based on their proximity. Distance Measurement also allows you to easily identify classes of objects in certain distance regions inside or outside a cell or touching the surface. In addition, a Distance Map may be used for measurements and further processing.

Compartments

• Segments can have "children"
• Individual segments can now have “child” segments. This removes the need to create groups for general parent/child relationships. Consequently, segments can have a count of associated objects based on distance or containment and can be tracked and further filtered in the pipeline. This supports easy and flexible workflows in a single pipeline run, such as “kiss-and-run” experiments with a combination of tracking and distance measurements or hierarchical relationships

Grouping

• This functionality is useful to combine multiple Analysis Operation outputs in a single step and is helpful in setting up user-specific statistical analysis.

Group by feature

• Segments can now be grouped by feature and sorted into subclasses.

Batch output

• In Batch Analysis, results of different image sets can be combined into one *.csv file. This is useful for data consisting of several image sets, such as multi-well plates, which all require the same analysis operation but need to be statistically analyzed altogether.

Magic Wand Improvements

• More intuitive click & create behavior in 2D and 3D Easy preview in the 4D viewer

Scalable Analysis - arivis Image Hub

• Scale up your image analysis with efficient batch processing on a server
• arivis Vision4D is now compatible with functions of the arivis Image Hub.

New Sample Pipelines and Pre-Installed Guides

• New Sample Pipelines have been added and all sample analysis pipelines for typical image analysis tasks have been updated. New pipelines:
• Detect cells or particles using seeded Region Growing
• Detect small structures using Watershed
• Compartmentalize cells or particles
• Comprehensive descriptions of these pipelines are now part of the installation and can be accessed via the help menu

Welcome to the arivis Vision4D 3.1.3 Release Notes - Version Date: Nov 23, 2019

What's new

• More easy installation of arivis Vision4D
• New licensing using a Softkey (Product Key)
• Easy license activation and management integrated in the arivis Vision4D Help menu
• Customers can much easier check for purchased license updates
• Hardware key still available on request
• ZEISS ZEN Bridge to arivis Vision4D
• Transfer and run sample or custom analysis pipelines from Zeiss Zen Blue (or any external application) to arivis Vision 4D with 2 clicks.

Bugfixes

• Distances operation continues to run in the pipeline, if the input of references is empty
• Re-trigger of 4D performance test after upgrade

Welcome to the arivis Vision4D 3.1.2 Release Notes - Version Date: Oct 08, 2019

Release 3.1.2

• Several fixes and improvement for import of several file types
• better support for tiled images
• improved performance for distance & compartmentalization operations and new option to limit calculation to the closest reference in distance calculations
• several fixes and improvements in analysis and measurement operations

Data Handling & Import

• new: reduced file size by using gzip compression by default for new SIS files
• improved: reliability for multi threaded data access
• improved: position accuracy for surface visualization
• fix: problem with distance matrix calculation for the Segment Colocaliziation operator
• fix: Membrane-Enhancement behaves correctly even with difficult parameters
• fix: avoid artefacts on textured clipping planes
• fix: the volume in the High Resolution Rendering was not clipped correctly sometimes
• fix: error handling for Objectness Measure Filter
• small fixes in the Intensity Profile

Analysis & Objects

• improved: performance for distance & compartment operations
• new: option to limit calculation to the closest reference in distance operation
• improved: performance for segment modification operation
• improved: export to CSV is more visible now
• improved: allow to directly switch the advanced analysis options on & off from the pipeline menu
• improved: parameter parsing in the Segment Tracker operation
• improved: indicator buttons in viewer label will open related panels if needed
• fix: correct tagging objects from multi channel labeled image import
• fix: potential problems in the Membrance Enhancement filter
• fix: prevent wrong error messages from histogram calculation job
• fix: potential problems with charts in master detail view
• fix: potential error in Membrane Segmenter operation
• fix: compartmentalization no longer adds children to parents multiple times
• fix: avoid technical message after upgrading an old pipeline with Blob Finder
• fix: avoid error with histogram calculation on float data
• fix: Segment Tracker - timepoint setting works better with Linear Regression and Conal Angle mode
• fix: arbitrarily structured ImageSets? & input ROI scaling
• fix: potential crash within the tag autocompletion

4D Viewer

• fix: potentially incorrect applied opacity
• fix: clipping planes & Z-scaling

Welcome to the arivis Vision4D 3.0.1 Release Notes - Version Date: Oct 05, 2018

Release 3.0.1

• reduced file size by using gzip compression by default for new SIS files
• improved reliability for multi-threaded data access
• improved position accuracy for surface visualization
• several fixes in distance matrix calculation (Coloc Operator), the Membrane-Enhancement and Objectness Measure Filters and clipping

General: New & improved & fixed

• new: reduced file size by using gzip compression by default for new SIS files
• improved: reliability for multi threaded data access
• improved: position accuracy for surface visualization
• fix: problem with distance matrix calculation for the Segment Colocaliziation operator
• fix: Membrane-Enhancement behaves correctly even with difficult parameters
• fix: avoid artefacts on textured clipping planes
• fix: the volume in the High Resolution Rendering was not clipped correctly sometimes
• fix: error handling for Objectness Measure Filter
• small fixes in the Intensity Profile

Welcome to the arivis Vision4D 2.12.5 Release Notes - Version Date: Jun 26, 2017

Visualization in the 4D Viewer

New & improved

• ​new: lighting setup is included in preferences
• new: lighting palette now has options for shininess
• new: point light option added
• new: ability to choose the timestamp font in movie export
• new: option to specify volumetric data and segment clipping separately
• new: ability to edit the Bleach Correction parameters for exponential fitting manually
• improved: handling for bookmarks from older arivis Vision4D versions
• improved: squad interpolation for Storyboard movie export rotations
• improved: display relative time stamp in exported movies

Analysis and Annotations

New & improved

• new: ability to do a pipeline run at downscaled image data resolution
• new: Background Subtraction operator
• new: completely reworked Store Annotation operator allows to handle multiple input at once
• new: Store Annotation operator will be added automatically
• new: ability to modify tags in the Store Annotation operator
• new: Store Annotation operator will keep annotation color
• new: option to keep stored annotations even if a pipeline undo is performed
• new: ability to copy selected annotations to Analysis or Document storage manually
• new: reworked Import Annotation operator UI with auto complete for tags
• new: reworked Annotation Mask operator with the option to choose by tag and tag auto complete
• new: ability to combine multiple segment or track filter in one pipeline step
• new: Ratio Filter is now part of the Segment Filter operator
• new: each operator in a pipeline can define color settings for the output
• new: a segmenter or tracker operator can customize the name pattern used for newly created annotations
• new: Export Annotation operator will show useful features only (depending on if the input are tracks or segments)
• new: Export Annotation operator will export the names of the tracks in group by track mode
• new: Coloc Filter exports filtered results only to the Excel file
• much improved Intensity Threshold UI
• improved: random color option is more random now
• improved: Dual Threshold Segmentation operator removed, required core intensity is now an optional parameter of the Intensity Threshold Segmentation operation
• improved: multi-threading support for Blob Finder
• improved: pipeline reconfiguration on pixel size or structure changes
• improved: a better structured context menu in the Annotation window

Import

• new: Slidebook (.sld) Media Handler
• new: VGI/VOL Media Handler

Misc

• new: viewer label shows scope name (if useful)
• movie export: regular video formats (avi, mp4) no longer show a warning when selected "
• measure option in the 2D Viewer has been renamed to "scale bar

Public Preview

These features or potential new modules are available as a free beta-version during our development process after which they may become purchasable modules. Feedback is very welcome ( support@arivis.com ) and will help to further develop the software.

• Interactive Feature Statistics in the Annotation window with Timeline View to sort, analyze and visualize tracks and features of segments along a track over time
• 3D Volume fusion & Landmark Registration (Scope Fusion)
• new: ability to run Scope Fusion at subsampled image data resolution
• new: copy & paste Scope Fusion transformation parameters
• new: ability to manually fine-tune landmark-based calculated transformation parameters in Scope Fusion
• new: last Scope Fusion settings are preserved as long as Vision4D is running
• improved: Audit trail entries for Scope Fusion
• new: Info Viewer shows Scope offset

Welcome to the arivis Vision4D 2.12.4 Release notes - Version Date: Dec 06, 2016

Visualization in the 4D Viewer

New & improved

• Export of 360° videos from the Storyboard
• Create 360° panoramic image in the High Resolution Dialog
• Isosurface extraction now allows a higher smoothing factor

Image Analysis & Annotations

New & improved

• Export of several segment features along a track using "Group by Track" in the export annotations operator
• Better use of memory for 3D filter operators for faster image processing
• Switched to ITK 64bit lib

File Format & Import & Data Handling

New & improved

• Improved BigDataViewer Import
• Possibility to edit the scope offset in the Info Viewer
• Tile Sorter grid option to place the first tile centered

Data Pre-Processing

New & improved

• Faster preview in the Transformation Gallery
• Python script command VolumeGetPoints

Welcome to the arivis Vision4D 2.12.3 Release notes - Version Date: October 10, 2016

Visualization in the 4D Viewer

New & improved

• Interactive split of segments in the 4D Viewer
• Possibility to join (merge) touching segments
• Delete key to remove several selected annotations
• Easier access of annotation visualization options in the settings bar (switching from surfaces to centroids)
• Preview for isosurface extraction
• Import and export of geometry objects as obj-files considering or ignoring pixel size
• Rename geometry items (via context menu or F2)
• Improved naming of default isosurface item
• Change color, visibility and clipping for geometry objects
• Synchronization of the XY plane in the navigator palette and the clipping plane in the 4D Viewer
• Improved usability of the 4D Channel Settings palette
• New opacity curve templates added for better visualization of faint structures (maximum intensity) and certain intensities (bandpass)
• Storyboard: allow setting for keyframe transitions to non-integers
• Storyboard: adjusted default parameters for faster movie export
• Option to inactivate interpolation (useful for rendering of histopathology z stacks)
• Supersampling for denoising movie and high resolution export can be enabled or disabled in the preferences
• Improved Render Settings palette
• Better interactivity of the 4D Viewer on change of color map settings

Image Analysis & Annotations

New & improved

• Annotation Visibility palette greatly enhanced and renamed to Annotation Settings
• Option to show all or selected annotations in the 2D or 4D Viewer
• Group segments by track in the annotation table
• Export annotation features to XLS grouped by track
• Copy feature values to clipboard
• Create a new segment or track filter based on the selected feature value
• Filter segments or tracks comparing feature by range
• New default unit is µm
• Time-based gradient color-coding of tracks or segment-color-based color-coding (in 2D & 4D)
• Open the Track Editor from the track's context menu in the Annotation window
• Ability to add or remove a tag to a group of selected annotations
• Batch Analysis: improved support for large number of annotations in the Add Region dialog
• Creation of missing folders for analysis export (if needed)
• Warning if an operator's preview is working with unprocessed data
• Improved: segmenter's preview is switching to the right input data first
• "Copy Annotations" renamed to "Duplicate Annotations"

File Format & Import & Data Handling

New & improved

• Transformation Gallery - Transformation and resampling of image data including cropping, rotation, change of bit depth and dimensions, flipping
• Drift correction using a track of a defined immobile object for more accurate quantitative analysis of drifting time lapse data
• Bleaching Correction for time lapse data
• Export complete scope rotated according to Sectional Plane from Projection Viewer
• new in Projection Viewer: Minimum Intensity Projection mode
• Olympus VSI media handler
• NDPI multi focus support
• Faster import for NDPI multi-channel data
• Option to import data into a GZIP compressed SIS
• Preventing a problem with Nifti data

General

• Improved User Guide PDF
• General stability and performance optimizations

Public Preview

These features or potential new modules are available as a free beta-version during our development process after which they may become purchasable modules.

Feature Statistics

• Interactive Feature Statistics in the Annotation window
• Timeline View in the Feature Statistics to sort, analyze and visualize tracks and features of segments along a track over time
• Segments of selected tracks automatically included
• Easy addition of connected segments (in a track) for selected segments

Scope Fusion & Landmark Registration

Welcome to the arivis Vision4D 2.12.2 Release notes - Version Date: June 16, 2016

Visualization in the 4D Viewer

New:

• Isosurface extraction now supports float datasets

Improved:

• Scaling for imported geometry

Fixed:

• Opacity curve problems with float data
• Improved 8bit mapping for float datasets
• Better error message if no isosurface could be extracted
• Surface quality now ensures proper caps
• Problems after switching from a float data to another dataset
• Individual plane offset is now preserved
• Issue causing a storyboard crash under very specific conditions
• Clipping intersection calculated wrongly
• Annotation clipping is now properly applied to movie export and screenshots
• Better support for float data with negative values
• Problems with wrong positioned tracks
• Ignoring the visibility attribute of annotations
• Import problems with storyboards including frame settings beyond the current scopes range

Image Analysis & Annotations

New:

• Blob Finder analysis operator to find cells or any other type of rounded cell organelles in a noisy image using automatic seed finding and a watershed algorithm in an easy-to-use 2 step process
• Creation of a new channel for the results of Analysis voxel filters and Colocalization groups

Improved:

• Error handling during geometry import

Fixed:

• Problems with the polyline edit tool in the Colocalisation Palette
• Misc display zoom & scroll problems
• Segment filter criteria disappears
• Annotation mask calculated wrongly for some datasets
• Segment colocalization calculation
• Sub-pixel accuracy for some features

File Format & Import & Data Handling

New:

• Invert z option for pre-processing in the Tile Sorter

Improved:

• updated Nikon ND2 SDK

Fixed:

• Stitching problems if the first tiles have a tile shift > 0 in the Tile Sorter
• Stitch Tiles dialog size in the Tile Sorter

General

• Colorbar better supports float datasets
• Info Viewer: Insert Plane allows to define negative offsets

Welcome to the arivis Vision4D 2.12 Release notes - Version Date: Jan 26, 2016

Visualization in the 4D Viewer

New

• Interactive “fly-through” mode that enables to visualize volumes from the inside
• Possibility to configure several clipping scenarios (Sectional Planes, Region of Interest, and clipping on Annotations)
• Insertion and combination of multiple Clipping Planes at different angles and time points
• 4D Surfaces: create, export & import 4D geometry objects based on Intensity threshold
• Show annotation independent from the Analysis module as 4D Surface
• 4D Bookmarks: allow to record, save, restore and share interesting visualization views and scene settings
• Possibility to export & import 4D Bookmarks
• Allow continuously spinning visualization (momentum)
• Lighting and Projection settings for better visualization in Volumetric rendering mode, projection and stereoscopic rendering
• Save, import & export of storyboards

Improved

• Storyboard with more flexible user interface for movie creation with generic export function and animation of channels, opacity, slicing and camera settings
• Quality and performance in 4D rendering with optimized multi-threaded data handling & caching
• More interactivity tools (e.g. rotate, move, select, fly-through) for fast and easy exploration of 3D/4D datasets

4D Surfaces: Create, export & import 4D geometry objects based on Intensity threshold

More and new interactivity tools for exploration of 3D/4D datasets

Show annotation independent from the Analysis module as 4D Surface

Image Analysis & Annotations

New

• Filtering by distance of objects and creation of annotation groups in the Analysis Pipeline
• Local Threshold Filter for improved segmentation in variable background
• Restoration Filter (Denoising)
• Inverted Annotation Mask for more analysis possibilities
• Definition of a threshold in the Colocalization Palette
• Visualization of Analysis Annotations (Segments) as bounding box, sphere or geometry

Improved

• Segmenter preview accuracy
• Handling for loading or deleting large amounts of annotations
• Sorting progress in the Annotation dialog

File Format & Import & Data Handling

New

• IED import is possible via menu File-> Import
• Export of the Audit trial (*.doc)
• Leica MediaHandler import of additional dimensions as scopes

Improved

• Support for different internal image formats in Mirax MRXS (e.g.BMP)

General

New

• Color Bar access in any Viewer type (2D and 4D)
• Alternative Color Bar visualization for data sets with many colors
• Palettes are categorized for easier access
• Add or remove channels by scripting
• Description for all script commands in the User Guide

Improved

• Frontend UI of Personal WebView to be used in any browser

These features or potential new modules are available as a free beta-version during our development process after which they may become purchasable modules.

Public Preview: Interactive Feature Statistics

These features or potential new modules are available as a free beta-version during our development process after which they may become purchasable modules.

• Visualization of distributions of one feature (bar chart or histogram) or two features (scatter plot)
• Color annotations based on feature distribution
• Export statistics as image

Welcome to the arivis Vision4D 2.11.2 release notes - Version Date: July 15, 2015

Analysis Pipeline & Annotations

New

• Filter annotations by current plane or frame in the Annotations window
• Specify custom analysis region by using selected annotation as a template
• Ability to specify working channel for each Analysis voxel operator
• Analysis operator to combine segments lists
• Ability to create a 3D segment from multiple 2D annotations
• Optional scalable sphere representation for annotations in 4D-Viewer
• CSV import for convolution filter kernel
• Geometric Centroid feature & ability to use for tracking
• Scripting for Annotations

Image Processing

Improved

• Matlab UI
• Syntax highlighting for Matlab scripts
• More documentation for Matlab scripts
• Better visualization for selected tracks in 2D
• Track Editor UI
• Scripting for Analysis Pipeline

File formats

New

• LaVision OME-TIFF mosaics
• LSM mosaics

General

New

• Ability to delete restore points
• Reclaim disk space by defragment a dataset
• Assign channel color mapping by wavelength

Improved

• Overall stability and performance for the TileSorter
• Frame timestamp visualization harmonized
• UI is more "flat" now
• Apply a time interval to all frames timestamp
• A lot of stability improvements for the Analysis Pipeline​

Fixes

• Coloc m1 & m2 calculation
• Artefacts in 3D Denoising Filter
• Changing frame timestamp in Info Viewer
• Preserve offset from FEI TIFFs on import
• Miscellaneous fixes and optimizations

Welcome to the arivis Vision4D 2.11 Release notes - Version Date: April 30, 2015

Analysis Pipeline, Image Processing & Annotations

New

• Analysis Pipeline UI renewed
• All voxel operations are temporary by default (keeps the original data safe and unchanged)
• Save voxel modification as a new scope or file if needed
• Define the input source for all of the segment or track operations (ability to branch)
• Interactive Track Editor allows you to correct or edits segments and cell tracks semi-automatically and visualizes segments tracked over multiple time points so you can edit, split and merge existing tracks
• Voxel mask with annotation
• Ability to rename pipeline operations to reflect the purpose
• Ability to import existing document annotation for further analysis
• Trainable Segmenter (Ilastik Classifier)
• True 3D filter: Denoise & Objectness Measure
• Unsharp Masking Filter
• More features (e.g. current frame, channel based intensity, …)
• Volume Mesh Exporter
• MATLAB Voxel Filter
• MATLAB Script Filter
• MATLAB Voxel Segmentation
• Operator to directly export results to Excel or CSV
• New unified annotation model used for document annotations and analysis results
• Completely new Annotations window with support for feature calculations
• Export annotation features to Excel or CSV
• Annotation Visibility Palette
• Switchable float on top window behaviour for Annotations window

Improved

• Dual Thresholding Segmenter with a third Core parameter
• Units for bounding box feature
• Optimized undo redo behavior for analysis operations
• Pipeline management
• Calculation precision
• Analysis scripting

Visualization in the 4D Viewer

New

• Solid navigational plane in the 4D Viewer

Improved

• Rendering and lighting
• 4D Storyboard Frame-Progression

General

New

• User Gradient entry in the Colorbar context menu
• Add or remove channels in the Info Viewer
• Ability to sync the selected annotations in split view mode

Improved

• Overall stability fixes & performance optimizations
• Internal refactoring to support upcoming cool new features and products

File formats & Data handling

New

• Aperio (SVS) Media Handler
• Batch Alignment for multiple planes in the Tile Sorter
• Row and colum displacement for grid layout in the Tile Sorter
• Mouse Wheel Zoom & Drag Tool in the Tile Sorter

Improved

• CZI import with support for AxioCam MR3
• Multi file CZI import
• Auto Color Range during import
• LSM import performance
• TIFF export

Misc

• improved IntensityProfile updates on data changes
• Personal Webview: reworked HTML frontend with support for touch events (e.g. on an iPad)

Fixes

• Color handling for DeltaVision import
• FEI Tiff import
• IntensityProfile for datasets with offsets
• ROI clipping problems