Release notes

• new: provide a description and an offline download for optional components in the installer
• fix: improved compatibility for DeltaVision DV import
• fix: What's New opens after an update more reliable
• fix: installer makes sure that no files from former Vision4D versions are left in the installation folder 
• additional small fixes and improvements in the arivis_dl library

• new: Draw Tool has a context menu and better keyboard shortcut support 
• new: Draw Tool is aware of the DL Training panel 
• new: Draw Tool allows to change class to draw by shortcut or context menu (in DL Trainer mode) 
• improved: Trace Tool - connect to a cell body segment 
• improved: Trace Tool - optimized remove branch 
• improved: 'unable to connect' messages in the Trace Tool are more understandable 

• new: 'Neuron Tracer' (from the Segmentation category) has been renamed to 'Neurite Tracer' 
• new: 'Neuron Tracer (from Cell Body)' has been renamed to 'Neuron Tracer' 
• new: Neuron Tracer preview shows all parts in the same color 
• new: Neuron Tracer preview shows the filtered parts slighly dimmed (instead of hiding them completely) 
• improved: parameter labels in the Neuron Tracer are more precise 
• improved: default threshold value and threshold warnings in the Neuron Tracer 
• improved: tooltips in the Neuron Tracer 
• fix: if the tracking operation had a lot of results, it could happen that the last tracks were not displayed 
• fix: prevent the creation of (almost) empty traces in the Neuron Tracer 
• fix: ensure that a preview progress label is always displayed immediately 

• new: display of starting points can be turned off for traces 
• improved: optimized cone generation for traces in 4D Viewer 
• improved: fallback to line based visualization if cones for traces would exceed memory 
• improved: remember last used Z-Projection value for trace visualization in 2D 
• fix: minor problem with RGB Projection in 4D Viewer 

• new: Wellplate Editor to manually assign imagesets to wells or fields of a well 
• new: semi-automatic assign imagesets to well or field positions based on the name of the imageset (in the Wellplate Editor) 
• new: additional import scenario to import wells as imagesets and open the Wellplate Editor afterwards (for manual assignemnt) 
• fix: some LaVision data could not be imported correctly for TileSorter 
• fix: problems with some CZI if imported for TileSorter

• new: Predictive Analytics service as optional install 
• new: gRPC service connector
• new: ZenBridge is able to work with gRPC service connector (optionally) 
• improved: included Sentinel driver and HASP Lib have been upgraded to version 8.5 
• fix: sort order in field selector of Navigator (for wellplate data) 
• fix: rare crash in the Transform Surface dialog 
• additional minor fixes and 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 3.6, 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 3.2 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 2.12.4 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 2.12.2 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 2.11 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