Release notes

New & Noteworthy

• New Multi Run for the Analysis Panel: run the pipeline for multiple wells or fields of a well plate document
• Retain selected tags when switching between wells or image sets
• Accurately detecting cells and nuclei of varying sizes with the new Cellpose-SAM model
• More intuitive rotation in 4D Viewer using the trackball rotation mode

High Content Analysis

• new: run an analysis pipeline for selected well or fields with the new Multi Run mode
• new: interactively select wells and fields for the analysis multi run with a new well picker
• new: show hierarchical state and progress while running a pipeline over multiple fields and wells
• new: explore the results of already finished wells while the pipeline for other wells is still running
• new: stick to the currently selected tag selection while switching between different wells or fields
• new: stick to the current channel visibility while switching between different wells or fields
• new: distinguish different image types for a single well or field (e.g. fluorescence z-stack, bright-field or maximum intensity projection)

Analysis

• new: Convert Traces to Segments operation
• new: Cellpose-SAM (CPSAM) model is available in the Cellpose-based Segmenter operation
• improved: Segment Morphology operation has additional parameters for some methods
• improved: show a warning in the Batch Analysis if output files with the same name would be generated (and would overwrite each other)
• improved: DL reconstruction speed up by better utilization of GPU resources
• improved: better progress while downloading models from arivis Cloud AI Model Store
• improved: error handling for the Export Surfaces operation
• fixed: some minor bugs for the ML Trainer (Objects) and ML Trainer (Image)
• fixed: issues with the objects in the DL Trainer if classes or training has been renamed before drawing
• fixed: potential problem with continue training if multiple image sets are used in the DL Trainer
• fixed: some rounding issues in the max distance field of the Compartments operation
• fixed: potential crash with Magic Wand on CZI data
• fixed: a problem with large planes in CZI data if used with arivis Cloud models in DL Segmenter
• fixed: do not reset the object selection when switching viewer types (while showing objects from the Analysis pipeline)

General

• new: do not reset object filter (e.g. selected tag) when switching between image sets
• new: do not reset channel visibility when switching between image sets (with the same number of channels)
• new: the Preview Features dialog allows you to activate and test early results for newly added features
• new: the arivis Pro help content is provided by the ZEISS help viewer now
• improved: help content layout

Objects

• new: ability to represent feature values as colorful bars normalized to min / max of the Summary (if enabled)
• improved: detection in the AI-assisted mode in the Draw Tool for data zoomed > 100%
• improved: selection of (overlapping) objects in 2D
• improved: help content for object store types and the context menu of the Objects dialog

4D Viewer

• new: Quick Movie Export - export like you see it in the viewer
• new: intuitive rotation of 3D data using the trackball rotation mode
• new: dedicated Rotate tool
• new: improved positioning of clipping planes with handles
• improved: cursor feedback for axis-specific rotation with right mouse and XYZ key
• improved: more anti-aliased selection line
• fixed: prevent artifacts on volume boundaries with inverted opacity curve
• fixed: prevent object render problems with some specific NVIDIA driver versions
• fixed: avoid problems with missing permissions for the clipboard on copy / paste of opacity settings

Data Handling & Import

• new: import image type for well plate data (e.g. fluorescence z-stack, bright-field or maximum intensity projection)
• new: include image type (if available) in the default name for the imported image set
• improved: import tiled LaVision FastTile Blaze data
• improved: normalization of the color range for CZI float datasets
• improved: support added for more compression types of HDF5 blocks (e.g. used by some IMS datasets)
• fixed: potential wrong colors were imported from some Aperio-SVS data
• fixed: wrong pixel size imported from some Aperio-SVS data
• fixed: import of different image types as channels from Yokogawa
• fixed: import of BigDataViewer with non-consecutive setups
• fixed: some CZI appear blank if opened but not imported

Misc

• new: Docker Desktop is now an optional download in the arivis Pro installer
• new: includes a Docker Desktop license covering running arivis Cloud models in arivis Pro
• removed: Extended Focus has been retired
• several additional bug fixes and stability improvements

New & Noteworthy

• AI-assisted mode for the Draw Tool - precision and efficiency in manual segmentation workflows.
• Import Document Objects operations allows to copy stored features.

Improvments & Fixes

improved: easier adding CZI data to Batch Analysis

improved: allow download of CZI data from arivis Hub

improved: DL Trainer behavior while drawing at different image sets

fix: object store cache for CZI data uses correct extension now (e.g. filename.czi.cache)

fix: wrong well or field assignment for some scenes in CZI data

fix: scaled analysis could cause artifacts with sparse CZIAnalysis:

fix: DL Trainer - drawn objects were colored wrong (if class was renamed before drawing)

fix: Compartments operations did not store the inputs correctly if the same input was in use multiple times

fix: intensity features are listed under the segments category again

fix: instance segmentation (working on modified channel data) writes results to the correct time point more stable

fix: using trace objects in Python script operation

General

improved: Draw tool visualizes the merging of shapes directly when drawing with the brush* change: arivis License Tool requires .Net 8 now* additional smaller fixes

New & Noteworthy

• AI-assisted Spine Tracing: automated spine detection using pre-trained Al models or other methods.
• Enhanced Cell Measurements: expanded measurement capabilities enabling richer feature sets.
• Native CZI Support: open, visualize and analyze CZI data, with no intermediate conversion steps needed.
• Remote Docker: run instance segmentation with the help of a satellite / remote Linux system.

Deep Learning / Machine Learning

• new: DL Trainer preview - verify the trained model right in the DL trainer panel
• new: tile blending option for DL reconstruction operation
• new: option to specify the normalization range to be applied on the data before inference
• new: confidence feature value for instance segmentation results
• new: option to run instance segmentation with the help of a remote Docker engine
• new: arivis Cloud preference page
• new: option to adjust normalization range for Cellpose operation
• improved: improved consistency for CUDA based calculations (e.g. Cellpose)
• improved: better help and guidance for running instance segmentation based on ZEISS arivis Cloud models
• improved: AI model store sorts list by creation time now
• improved: AI models store displays the model's author
• improved: do not show and store arivis Cloud access token in clear text anymore
• improved: order of classes in the DL trainer is reversed (the same as in arivis Cloud now)
• fix: prevent "Could not reach the instance segmentation service" for some specific Docker setups
• fix: ML Segmenter - under some conditions, segments were not found on the last plane
• removed: sync with channel visibility in ML Trainer

Tracing

• new: Spine Tracer operation to detect spines and extend existing traces
• new: AI assisted spine detection in the Spine Tracer operation
• new: spine counting and spine density object features
• new: SWC export respects selection
• fix: Neuron Tracer - make sure all neurites are connected to a cell body (if configured)

Analysis & Objects

• new: SD (standard deviation) added for a lot of features
• new: morphological segment features (convex hull, cross section area, equivalent ellipse projection, maximum inscribed sphere, inscribed disk)
• new: additional 2D segment features (symmetry 2D, Feret projection, convex hull projection)
• improved: Seeded Region Growing supports more and larger seeds
• improved: object styles parent filter allows to select trace type
• improved: updated ITK version (fixes cancellation issues)
• improved: progress in the Store Objects operation during surface pre-calculation
• improved: error handling in the Import Surfaces dialog
• improved: group statistics for traces
• improved: more detailed descriptions for object feature calculations in the help

4D-Viewer

• new: arivis Pro tries to active high performance graphics automatically
• improved: optimized progressive strategy for object visualization
• improved: surface calculation creates smoother objects with less terracing artefacts
• improved: selection of objects behind an active clipping plane
• improved: unified memory limit warnings for traces and segments
• improved: performance for the track tool in 4D
• fix: avoid block artefacts for storyboard movies with time series data

Data Handling & Import

• new: open CZI data natively without the need for import
• new: Thermo Fisher CellInsight CX7 media handler
• improved: background correction performance for large data
• improved: Meta Image Series / ImageXpress import
• improved: support for JPEG2000 compressed TIFF data
• fix: image set names for well plate datasets (e.g. from ImageXpress or Yokogawa)
• fix: potential import problems for 32bit float TIFF data
• fix: problems importing multimodal Yokogawa data
• fix: some VSI were imported with a wrong channel order
• fix: potential problems with export objects as labelled images
• fix: import *.am data from Avizio
• fix: import of stitched LaVision datasets

General

• new: unified Pan tool (previously Drag tool in 2D)
• new: allow panning in 2D and 4D Viewer (independent of the active tool) by middle mouse drag
• fix: prevent selection of non editable objects in the Draw Tool (e.g. track or trace)
• removed: deprecated Python script API functions ImageSet.get_pixel and ImageSet.set_pixel
• switched to .Net 8 * numerous additional bug fixes and stability improvements

ZEISS arivis Pro 4.2 (formerly Vision4D) offers users the freedom to select the most suitable image analysis method for their needs. The new release includes enhanced AI-driven tools, 3D analysis capabilities, and large dataset handling. The software allows for unprecedented flexibility to tailor microscopy image analysis workflows to answer research questions.

New & Noteworthy

• Optimized meshing and rendering for unlimited numbers of objects in the 4D Viewer 
• Instance (object-based) segmentation driven by Deep Learning models from arivis Cloud AI Model Store
• Cells and nuclei segmentation in microscopy images using the Cellpose operation 
• High precision preview in the Analysis Pipeline can work on 3D data to produce a more meaningful preview

Other Optimizations

• Analysis can directly show a preview in the 4D Viewer for object creation operations (e.g. Neuron Tracer)
• Machine Learning can auto-optimize the used feature set to improve performance
• Improved handling for huge amounts of objects in the objects table
• Rebranding is completed: The software is now called ZEISS arivis Pro

Cellpose Segmenter

• improved: better memory checks to avoid internal errors
• improved: more clear error and warnings
• improved: better description of the available pre-trained models in the help
• change: perform planewise is enabled by default now
• fix: handling of results for time points other than the first one (in combination with voxel filters)
• fix: normalization for data with bias in min intensity value
• fix: other small fixes for the Cellpose Segmenter

Import

• improved: importing channel names for XDCE data
• fix: import problems for some ND2 time series

General

• improved: faster free consumed license after quit of the application