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 3.6.1, 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

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 3.4 Release Notes - Version Date: 18 January, 2021

Top Features

• New License Manager with a better overview of all licenses
• Machine Learning improvements (for multiple images sets)
• Easier to use and start of analysis with the new operation list, search options
• New Image and Object Math operations
• Python 3 Scripting support

4D Viewer

• Storyboard can export 4k movies (h264)
• improved sampling options in the preferences
• better surface quality for very small or thin structures

Analysis & Objects

• Redesigned operation list with short descriptions, categories, and search functionality
• New Image Math operation - do calculations between channels, planes, and timepoints
• New Object Math operation allows to subtract, merge or intersect object
• Improved and better-structured selection of input channels
• Newly created channels can be used in the same pipeline immediately
• Object Feature "Relative Volume" - volume percentage of the total volume
• Split objects by shape (w/o Analysis Pipeline)
• Much faster loading and sorting of objects in the objects table
• Speed of interpolation in the Draw Objects tool
• Basic support for high precision marker objects (created with arivis VisionVR)

Machine Learning Improvements

• Ability to define and use machine learning classes across several image sets
• Training for different pixel scaling
• for more speed
• more coarse textures detectable
• Redesigned feature dialog
• Better compatibility with the import of Ilastik trainings
• General speed improvements:
• Machine Learning operator now makes better use of available CPU cores (speed improvement for >10 CPU)
• Better compatibility for imported Ilastik Machine Learning trainings

Scripting Improvements

• Scripting in Vision4D (Script Editor) has been updated to Python 3
• NumPy is now part of the embedded Python 3 environment
• New Python integration with better support for debugging and external Python installations
• Script support for export and import of labeled images
• Run Deep Learning networks in arivis Vision4D:
• Python package and startup documentation supplied to run a prepared Tensor Flow library with V4D 3.4 via Python. This allows also non-experts in Python and Deep Learning to use established Deep Learning networks in facilities.

General

• The new License Manager allows to select a specific Vision4D license on startup
• Import of Imspector OBF/MSR data
• Support for the newest Lavision OME format
• Check whether an imported file should be discarded or kept when closing
• Color settings:
• Apply color settings to all image sets
• Perform Auto Color Range over all image sets
• Ability to reset color settings

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 3.1.4 Release Notes - Version Date: Feb 11, 2020

4D Viewer

• New: 4D View Control Panel

Data Handling and import

• Fix: issues with some Imaris and BigDataViewer files written by third-party software
• Fix: reduced memory footprint while importing multi-scene *.ims files

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 2.12.6 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 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