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, released 11 February 2022.

New & Noteworthy:

• New: Deep Learning inference operations in the Analysis Pipeline
• New: better support for Wellplate data with the new Well Picker panel
• Improved: Blob Finder analysis operation

Deep Learning:

• New: Deep Learning inference with GPU support (CUDA)
• New: use trained deep learning models to do image reconstruction in the Analysis Pipeline
• New: use trained deep learning models in the Analysis Pipeline to segment images
• New: support for the Open Neural Network Exchange (ONNX) format
• New: support for CZMODEL / CZANN Model Specification providing interoperability with ZEN and APEER

Analysis & Objects:

• New: Blob Finder normalization can now be parameterized in more detail
• New: exponential mapping for Blob Finder normalization
• New: allow manual range for Blob Finder normalization
• Improved: Blob Finder progress better reflects normalization step
• Fix: possible problems with Blob Finder preview
• Fix: prevent wrong execution in Blob Finder which leads to strange patterns
• Fix: incorrect progress after stop of the Blob Finder operation
• Fix: surprisingly incorrect results after Split Object
• Fix: save/restore modified object name pattern

Import & Data Handling:

• New: export image data to OME Tiff
• New: Well Picker panel allows to switch between images sets of a well plate easily
• New: Navigator panel shows well plate coordinates for images sets of a well plate
• New: support for ZSTD compression in CZI import
• Fix: rare problems with importing SVS files
• Fix: scenes order for CZI imports

General

• New: arivis is a ZEISS company now
• New: ability to select a specific GPU to be used for Machine Learning
• Improved: better explanation when GPU support for Machine Learning is not available

Summary of important changes in arivis Vision4D 3.5 which was released 2nd Aug 2021.

Top new features:

• New Object Styles to define object's color, transparency, material, and representation by tag
• Analysis Home screen with better access to sample pipelines
• Machine Learning Object Classification and performance improvements in all ML tools (incl. GPU/CUDA support)
• reworked Compartments operation supporting parent-child relationship with subjects within a certain distance and fast feature definition per level of hierarchy
• analysis pipeline operations implemented as Python script
• arivis VisionHub integration

General:

• "What's new" intro screen
• arivis VisionHub integration (up and download of pipelines, images and objects from/to VisionHub)
• significantly faster SIS save (structural modifications)
• Fix: incorrect scalebar length at certain pixel size ratios
• Windows 7 is no longer supported

Import & Data Handling:

• better support for import of HCA well plate datasets:
• Zeiss CZI well plate datasets
• GE XDCE datasets
• Yokogawa MLF and MMD datasets
• support for import of ND2 float data
• improved Nikon ND2 import using the latest ND2Read SDK
• better support for importing Leica LEI time series
• Olympus import using the latest IDAL library
• improved edit support for tiles in manual mode of the Tile Sorter
• much faster handling of a very large number of files to import
• Fix: rare issue where old metadata prevented SIS from opening
• Fix: Tile Sorter showing projection will update thumbnail after changing z-shift of a til

4D Viewer:

• New glass material style for object visualization
• improved and simplified lightings settings
• unified clipping planes front/back orientation
• 360° video export in 4K resolution
• Fix: end marker for 3D polyline objects
• Fix: prevent wrong positioned objects created with the Drop Objects tool in MIP view mode

Analysis:

• Improved Import Document Objects operation
• Analysis Home Screen provides a well-organized starting point for your analyses
• reworked input/output handling with support for multiple outputs from one operation
• Tracking provides secondary output for tracked segments and optional output for non tracked
• Seeded Region Growing provides optional output for the seeds
• reworked and redesigned Compartments operation
• Compartments operation supports creating parent-child relationships with subjects within a certain distance
• Compartments operation may classify objects as inside, intersecting, or proximal to the reference
• Compartments operation provide optional outputs for different relation subgroups
• The Compartments operation now supports the easy creation of Custom Features (e.g. count of children or mean intensity) for contained children
• Combine Outputs operation supports more than two inputs
• Machine Learning Object Classification analysis operation with different classes as separate outputs
• Visualize the disk location for temporary analysis files in the status bar
• Warning if the free disk space might be exceeded on running an analysis pipeline
• changed: No auto-select of a different input channel if the configured one is missing (warning for existing pipelines not fitting the data)
• A new analysis pipeline operations to use a Python script to
• run a voxel operation or to
• create or to
• Modify segments

Performance:

• improved: speed up segment creation for 2D data by avoiding surface precalculations
• much increased performance when creating or modifying complex segment structures

Batch analysis:

• allow to switch to batch analysis with the pipeline just configured
• remember last batch analysis output folder
• improved batch analysis configuration guidance
• changed: use all image sets by default in batch analysis when adding new files
• Fix: avoid potential problems working with a large number of objects (>10 million)
• Fix: prevent unintentional jumping of the view during execution of the analysis pipeline step by step
• Fix: preview for the Region Growing operation
• Fix: potential problem with inconsistent error messages
• Fix: avoid potential hang of the Membrane Detection operation
• Fix: bug in Image Math which could cause strange pattern
• Fix: potential crash with the ML segmenter
• Fix: prevent missing entries in the Export Object Features operation (edge cases)
• Fix: problem with saving the pipeline if some special Custom Compute Features are involved

Machine Learning:

• New Machine Learning Object Classification Trainer
• Run Machine Learning Object Classification to classify visible objects (no Analysis Pipeline needed)
• ML Trainer (Image) allows to paint into a class other than the one displayed
• ML Trainer (Image) - warning about 3D-features preview inaccuracy
• ML Segmentation provides classes as separate outputs in the analysis pipeline
• Machine Learning image operations benefit from CUDA hardware acceleration (if available)
• Much improved Machine Learning (Image) performance

Objects:

• New Object Styles allow to define the visual style of objects more easily including color, opacity, material and representation (surface, centroid or approximation)
• Setting of objects styles by tag with the new Object Styles Dialog
• Support for individual transparencies, colors and display type for single objects
• Option to ignore scope offsets while copying objects
• Tags are shown per image set
• Fix: rare problem with the magic wand mode of the Manual Track tool
• Fix: show color by time or by segment mode indication in the object table
• Fix: prevent unexpected disappearance of feature columns

Scripting:

• Integrated debugger for the Python script editor
• SegmentBuilder script support
• Dedicated scripting log
• Preference to define script log verbosity
• Scripting of object styles
• Clean up of script API
• More detailed script API documentation
• Improved Script editor help pane UI
• Fix: potential problem in handling pixel size

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 2.12.6 Release Notes - Version Date: Aug 18, 2017

Visualization in the 4D Viewer

New & improved & fixed in the 4D Viewer and Storyboard

• new: an option to turn off spline interpolation for the camera in the storyboard to avoid wiggling of the image for a still image in a movie.
• improved: keyframe interpolation in the Storyboard
• fix: momentum is now disabled during exports
• fix: warning before clearing the storyboard
• fix: closing the storyboard no longer clears keyframes
• fix: jumping between keyframes now works more reliably
• fix: channels properly initialized before exporting a movie (Storyboard)

General

• improved: NIfTI import (support for very large files)
• fix: parsing for Olympus VSI series names
• improved: error checking for Background Correction
• fix: potential problems with the tag auto complete in the Analysis Pipeline
• minor stability fixes and improvements for special data sets

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 2.12.1 Release notes - Version Date: Apr 29, 2016

Visualization in the 4D Viewer

New

• Restore 4D settings when switching between different viewers, scopes and the Analysis Pipeline
• 4D Clipping Planes available as Sectional Plane in the Projection Viewer
• Lighting and projection included in bookmarks
• Different mouse cursors for the different 4D tools
• Cursor feedback if the mouse hovers over an object
• Multi-selection for geometry and annotations using the shift key
• Deselect objects by left click in an empty space
• Auto-size centroids as a visualization option for annotations to approximate object dimensions
• Option to specify mesh quality of annotation objects
• Option to specify the amount of smoothing to be applied to annotation objects or isosurfaces upon extraction
• Simplified measure options in the Settings Bar
• Option to disable momentum
• Option to set custom color for isosurface extraction
• Keyboard shortcuts for Storyboard actions
• Video encoder now offers PNG support

Improved

• Storyboard: Improved and much faster movie export by introduction of GPU caching strategies
• Overall support for 32-bit float datasets
• Improved 4D visualization of annotations
• Better handling of opacity in 4D Channel Settings
• Better visibility and logarithmic scaling of histogram in 4D Channel Settings
• Restructured Annotation visualization options in the 4D Settings Bar
• Geometry palette and isosurface extraction user interface improved
• Bookmark sorting improved
• 'Slices' renamed to 'Clipping' in storyboard
• Various fixes and optimizations regarding geometry, clipping and annotations

4D Geometry- more options to visualize and extract Iso-surfaces

Multiple Sectional Planes visualized in the Projection Viewer

Image Analysis & Annotations

New

• Batch Processing Analysis for unattended execution of a pre-configured arivis analysis pipeline on a series of images
• Analysis Pipeline: Segment Colocalization Operator with export of distance table in Excel
• Analysis Pipeline: Improved Result Storage Operator with an option to save individual voxel filter results to a new file or scope
• Particle Enhancement Filter 3D to find to find rounded particles in a noisy image
• Possibility to run the Analysis Pipeline up to certain operation
• Analysis Pipeline: Fast Access to context sensitive help (F1) for single operators in the pipeline

Improved

• Restoration Filter has been renamed to Partical Enhancement Filter (2D)
• Touching Edge Segment Filter improved
• Track Editor shows the current track at the current frame upon opening

Batch Processing Analysis for unattended execution of an pre-configured arivis analysis pipeline for a number of data sets

Better visualization and more options to find tracks and segments

File Format & Import & Data Handling

New

• Import: Olympus OIR media handler
• Tile sorter: support for manual rotation of tiles and plane shift for tile stacks
• Tile Sorter: support for source data with tiles organized as scopes

Improved

• LIF import with stage positions

General

New

• Custom Gradient dialog with a preview option to check the result beforehand
• Color gradient template files accessible as preset directly in the Color Bar and in the Custom Gradient dialog
• System Check Utility directly accessible from Vision4D help menu

Improved

• UI layout for scaled displays with size set to 125%
• Better visibility of histogram in the Color Curve Palette

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