Release Notes

Released: 2026-03-20

Well Plate Analysis & Data Aggregation

• New data aggregation operation for wellplates - Heatmaps now use the aggregation data defined in your arivis Pro pipeline, replacing the previous approach using Export Object Features operation. Get the same results and matching color scales as in arivis Pro.
• Field-level and well-level data exploration - Browse aggregation results at both the well level and the individual field level, with export options for each.
• Automatic Excel-to-CSV conversion for export data - Pipelines using Excel (.xlsx) export are now automatically converted to CSV for seamless viewing in arivis Hub. No need to manually switch the export format in your arivis Pro pipeline.
• Configurable "separate workflow per dataset" default - Administrators can now set the default state of the "Create separate workflow run for each dataset" checkbox, helping HCA users avoid accidentally processing multiple wellplates in a single workflow. Note, can be configured to be off by default for customers who do not work with wellplates.

Region of Interest (ROI) Support

• ROI support in workflow creation - Workflows now respect the Region of Interest defined in your arivis Pro pipeline. Batch analyze specific regions of your datasets rather than processing the full image, saving processing time and focusing on areas of interest. Note, all fields must have the same dimensions in X and Y.

Analysis Compatibility

• Backward-compatible analysis mode – As before, to avail of all of the latest improvements, pipelines are automatically migrated to the latest version when the system is updated. A new configuration option allows customers to keep their analysis pipelines running in the old behavior and keep results consistent when updating between versions. If this option is required, contact support and make this request before scheduling the update to the latest version.

Security Improvements

• Cross-Site Scripting (XSS) protection - Input sanitization has been applied across all name and description fields to prevent stored XSS vulnerabilities.
• Strengthened authorization controls - Access to administrative functions is now properly restricted to users with the appropriate permissions. Unauthorized users can no longer access admin pages or modify user accounts via the API.

Fixes

• Auto-naming of custom features with the same name.
• Field numbers appear in random order in Field level CSV file.
• Fixed duplicate columns in export csv - PlateID, Well ID and field columns are no longer duplicated in Hub if they are already selected in pipeline.
• Fixes in the analysis - Improvements and fixes in analysis bring the same benefits when running analysis on arivis Hub. Refer to the arivis Pro release notes section on Analysis for a full list of all new feature, improvements and fixes.

New & Noteworthy

Accurately detecting cells and nuclei of varying sizes with the new Cellpose-SAM model.

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: DL reconstruction speed up by better utilization of GPU resources.
• improved: error handling for the Export Surfaces operation.
• fixed: a problem with large planes in CZI data if used with arivis Cloud models in DL Segmenter.

Data Handling & Import

• 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.

Fixes

• added host config to database config which resolves file lock during workflow execution.
• added RGB48/BGR48 support.
• fixed access violation return code.
• fixed dependency handling across all repos.
• added indexes to models for better performance for viewing workflow results.
• added configurable timeout settings for S3 watcher for better handling of large downloads from S3 bucket.

What’s new

Support for advanced instance segmentation in cloud environments (AWS, Azure).

• Integrate arivis Cloud models in your pipelines and run at scale

Native CZI support for analysis

• Run pipelines directly on CZI images; no conversion to SIS needed.
• Respect the arivisPro 4.3 naming of objects and metadata files for CZI Improved

Improved

• Improved image loading performance in browser when reviewing wells
• Workflow setup: increased max limit of shown workflow sub-executions from 100 lines to 1000
• Add cellpose and spinetracer operations for gpu support

Fixes

• Yokogawa .mmd and .mlf images after import have difference in sub-image order, channel color and metadata
• Yokogawa-Import: Brightfield image replaces first plane of lightsheet z-stack
• Fixed Z pixel metadata missing for Yokogawa image with .mmd
• Fixed well ID missing from imageset name
• Fixed issue with some sub-executions stuck at 100%
• Fixed: Merged csvs from multiple export operations have same name
• Fixed: issue with analysis objects not shown in viewer when Segments parameter in Results Storages operation is set to Result Image

New features added

• Disable selection of incompatible pipelines with incompatibility error in pipeline view.
• Add check for incompatibility errors and show errors in Workflowrun view.
• Add pipeline compatibility check between ariviHub and arivisPro versions.

Deep Learning / Machine Learning

• fix: respect "allow holes" setting for DL segmenter operation.
• fix: properly consider offsets to prevent tiling artefacts in the results of the Cellpose operation.

Analysis

• fix: problems with the Cellpose when create group is selected in ‘segment morphology’ operation.
• fix: prevent potential stuck of the store objects operation.
• fix: avoid error with constant mode in Image Math operation.
• fix: memory leak in machine learning segmenter.
• fix: precalculate surfaces in Store Objects operation.
• fix: fallback to CPU when CUDA device is missing. For e.g. when running DL operations such as Cellpose.

Import

• fix: brightfield image replacing first plane of z-stack on Yokogawa
• improved: better recognition of time series in CZI
• improved: compatibilty for LaVision data
• improved: import field offsets and apply transformations from Perkin Elmer data

General

• Missing CSV and View Object buttons for workflow results.
• Improve performance and reduce API call in Pipeline View.

New Features Added

• Added CX7 import support
• Support for grouping of workflow runs
• Addition of "group" column to workflowRunListView
• Group filter on workflowRunListView
• Edit dialog to change name and group of a workflowRun
• Support for workflowRun group on datasetGroup auto-analysis
• Support for workflowRun group on workflowRun creation
• WorkflowRun group feature can be disabled by the .env parameter NUXT_PUBLIC_DISABLE_WORKFLOW_RUN_GROUPS
• Support for changing AWS S3 credentials without api-server restart
• Added reporting features (status report, disk size)
• Allow cancellation of jobs (feature disabled by default)
• Addition of stopWorkerJob queue to BullMQ Arena configuration for job cancellation
• Ensured native czi analysis works in docker container
• Arivis 4.2 support
• ARIVIS42_COMPAT component environment variable used for objectserver and arivis-server adoption
• Enable move of NPM to %ALLUSERSPROFILE%, allowing npm/pm2 to run independent of user profile (requirement on many managed servers)
• Addition of deleteFile queue to bullmq-viewer
• Added copy to clipboard button in the screenshot panel (download and copy button are configurable)

Changes to Existing Source Code

• Resolved issue with worker scaling via Terraform for AWS
• Enhanced deletion handling of datasets, object files, and orphaned datasets
• Adjusted file naming templates to handle long file names and commas in CSV files
• Improved analysis job usage (correct queue, handle duplicate serverTaskIds)
• Aligned IMPORT_SUPPORTED_FILETYPES with deletable formats
• Changed data type to BIGINT for subExecutionDurationMs and processingDurationMs
• Improved logging for audit trail handling
• Addressed missing Z pixel metadata in Yokogawa CPf (.mmd) from image container detector
• Allowed longer mainFileS3Uri entries in the AWS S3 Sync database table
• Updated imageModule version to 3.4.9 ArivisHub 4.2.0 Copyright © Carl Zeiss, 2002-2024. All rights reserved
• Improved image container detector
• Added missing file formats for deletion
• Moved path correction into container detector
• Resolved double path encoding error and repaired recursive readDir in File Watcher
• Prevented caching of invalid file-handles
• Increased TILESERVER_FILE_HANDLE_CLOSE_TIMEOUT_MS to 2 minutes to prevent premature file handle closure
• Disabled dispose() logs and added logger.time to waitForFileHandlesToClose
• Added REDIS_MESSAGE_QUEUE_DATABASE to .env.defaults
• Disabled deletion worker by default and prevented recurring redis connection error messages
• Repaired hapi logger error on startup
• Disabled minimization on Webpack build to fix startup error with awilix on Webpack bundle
• Updated TileServer build pipeline to allow the option to publish to artifacts
• Frontend improvements for dataset filtering and displaying performance
• Added UX improvements for the dataset delete dialog
• Fixed the wrong number of subimages
• Removed splitting folder name by backslash
• Displayed error returned from api-server/listDirectories in the Sync AWS S3 Folder dialog
• Updated compatibility error check for the page analysis pipelines to version 4.2 and adjusted the error text
• Repaired pipeline description text overflow on the tooltip
• Changed time format for the duration in the workflow run list
• Ensured deletion of workflow runs is possible only for creators or admins
• Showed default image when a dataset is not available
• Aligned NUXT_PUBLIC_IMPORT_SUPPORTED_FILETYPES with deletable formats
• Upgraded @vueuse to the latest version
• Fixed build error after cookie-es update
• Supported ArivisServer 4.2 (adopted error handling rules)
• Improved error handling if pixel type is not supported
• Updated tools to the newest versions
• Activated gzip compression as a default option (Changed PROXYSERVER_USE_COMPRESSION variable in the .env.defaults file to true)
• Improved .env generated file on package creation:
• Added section for individual changes
• Repaired value for AUDITTRAILSERVER_CMD