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      AVITI™ OS 4.1.0 Release Notes

      Please Note: Several gating software releases precede this release.

      AOS 3.4.2 gates AOS 3.4.3, which in turn gates AOS 4.1.0. If updating your system from an earlier version, the user must install each gating release before the later version can be installed.

      The user may decide when to apply these updates.

      We recommend users initiate the update during a period of instrument downtime. During the update process, the system may restart multiple times and will request a power cycle when the update is complete.

      If the upgrade process does not complete within 3 hours, please contact ElemBio Support at support@elembio.com.

      Summary of Changes

      AVITI OS v4.1.0

      Applies to all instruments (AVITI LT, AVITI, and AVITI24™)

      Trinity™ Workflow improvements

      • IAL support for Trinity workflows: Individually Addressable Lane (“IAL”) is now supported for Trinity workflows, enabling per-lane library loading and configuration within a single run.

      • Support for IAL per-lane panels: Trinity workflows now support per-lane panel assignment, allowing each individually addressable lane to run a distinct panel within the same flow cell.

      • Support for uploading a custom BED file: Users can now upload a custom BED file when configuring Trinity workflows, allowing target regions to be defined outside of the standard panel offerings.

      Sustaining Features

      • New Service Wash available: A new Service Wash is now available to help clear clogs that may develop within the fluidics system, improving instrument uptime and reducing the need for service intervention.

      • New metric displayed in AOS and EBC: Occupancy Score: AOS and ElemBio™ Cloud (“EBC”) now display a new Occupancy Score metric, providing users with additional insight into run quality. Occupancy score measures how much of the imaging area is filled by polony signal across the sequencing channels.

      • Maintenance Mode (Maintenance and Tools): Instrument Door Controls and Network Health Check: Maintenance Mode now includes Instrument Door Controls and a Network Health Check under Maintenance and Tools, allowing users to manage door states and verify network connectivity directly from within AOS.

      • Offline log updates: Automatic log export has been removed from offline log handling, and the ability to export run logs directly has been added, giving users more control over when and which logs are exported.

      • Detection of the reagent cartridge without the optical sensor: AOS now detects the presence of the reagent cartridge without relying on the optical sensor.

      • Post wash changes: Fixed an issue where, on runs without indexing, some leftover reagent could remain in the instrument lines after the post-run wash. The wash now clears the lines on every run, helping ensure consistent data quality on your next run.

      Firmware Reliability

      • CAB firmware update to support an uptime monitor: The CAB firmware has been updated to include an uptime monitor, allowing AOS to differentiate between a full system reboot and a computer-only reboot.

      • Updated firmware to improve MAD TEC power efficiency: Firmware updates improve the power efficiency of the MAD TEC, reducing overall power draw.

      • Updated firmware to potentially reduce Hardware Malfunction and Hardware Interface failures: Additional firmware updates target a reduction in the frequency of Hardware Malfunction and Hardware Interface failures.

      Applies to AVITI24 Instruments

      • CNN low density fixes: Fixes have been implemented to address convolutional neural network (“CNN”) base calling issues observed in low-density regions.

      • Cytos™ Launch: The Cytos Cell Screening workflows will replace Teton™ workflows and fall under a broader “Multiomics” umbrella.

      • Deprecation of Teton and associated workflows: The Teton, Teton Atlas™, Custom Antibody Screening Kit, and Onboard Optimization workflows have been deprecated and are no longer supported in this release. The term “Cytoprofiling” has also been retired and will no longer be used.

      • Multi-cartridge workflow support: AVITI24 now supports workflows that span multiple Cytos cartridges, expanding the range of assay configurations available to users.

      • Support for the following Cytos workflows:

        • Optimization (1 cartridge)

        • Protein Screening (1 cartridge)

        • Optical Pooled Screening (OPS) (1 cartridge)

        • 3’ Transcriptome (1 cartridge)

        • Protein + OPS (2 cartridges)

        • Protein + 3’ Transcriptome (2 cartridges)

        • Multimodal Pooled Screening (MPS) (1 cartridge)

        • Protein + MPS (2 cartridges)

      • Support to run and visualize IF protein workflow: Users can now run and visualize the immunofluorescence (“IF”) protein workflow directly within AOS.

      • Visualization of well-based and cell segmentation thumbnails: AOS now displays well-based thumbnails as well as cell segmentation thumbnails inside each well, improving visual quality control of Cytos runs.

      • Ability to apply advanced settings:

        • Save raw projections

        • Save per-target background images for IF proteins

        • Apply illumination correction to images

      • Onboard SpatialData object generation: AOS now generates SpatialData objects onboard, streamlining downstream spatial analysis workflows.

      Recipe Changes

      • Updated post-wash recipe: (applies to all instruments) Fixed an issue where, on runs without indexing, some leftover reagent could remain in the instrument lines after the post-run wash. The wash now clears the lines on every run, helping ensure consistent data quality on your next run.

      Known Issues, v4.1.0:

      • A failed upgrade from AOS previous versions may result in a failure to auto-initialize. If you encounter this issue, please contact support@elembio.com.

      • If an upgrade from AOS v3.4.2 to v3.4.3 fails and the system rolls back to v3.4.2, the instrument may display a notification indicating the update was successful. If this occurs, please confirm your AOS version and, if it still shows v3.4.2, attempt the update again to complete the upgrade to v3.4.3.

      • Simultaneous leak errors on both sides of the instrument prevent AVITI OS from unlocking the waste module door.

      • Runs can proceed even if polony map generation fails under specific undetected conditions.

      • The UI may begin to lag after several days of uptime. If this occurs, refresh the UI by pressing Ctrl+Shift+Z on a connected keyboard. Logging out and back in, or power cycling the instrument, will also resolve the issue. To help prevent this issue, power cycle the instrument once per week as recommended in the instrument user guide.

      • After extended instrument uptime, the UI may go blank. This is a UI issue only; the run will finish without impact. If this occurs, wait until the light bar or ElemBio Cloud indicates the run is complete, then power cycle the instrument. To help prevent this issue, power cycle the instrument once per week. A fix is planned for AOS v4.1.1.

      Dependency Updates, v4.1.0:

      Additional software updates accompany AOS 4.1.0. Please ensure you update the following software and review the corresponding release notes: