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      AVITI™ OS 3.4.0, 3.4.1, 3.4.2, 3.4.3 Release Notes

      Please Note: AOS v3.4.3 is a required (gating) release and must be installed before any future instrument software updates. The user may decide when to apply this update.

      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 v3.4.3

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

      System Reliability

      • Corrected high-altitude wash timing: Fixed an issue causing incorrect wash durations at high-altitude installations.

      • Improved unexpected reboot monitoring: Improved the system's ability to detect and accurately report unexpected reboots.

      • Enhanced diagnostic data capture: Improved the system's ability to capture instrument diagnostic information after a crash or reboot, helping ElemBio™ Support resolve issues more quickly.

      Firmware Reliability

      • Improved run robustness: Addressed a rare mid-cycle timeout condition that could result in a Hardware Malfunction Error during a run.

      • Syringe acceleration adjustment: Slowed syringe acceleration to improve mechanical reliability.

      • More reliable crash diagnostics: Improved the system's ability to capture instrument diagnostic information following an unexpected crash.

      • Reduced instrument diagnostic logging noise: Improved internal system logging for easier troubleshooting.

      Recipe Changes

      • Additional post-run wash step: Individually Addressable Lane (IAL) recipes now include an additional wash step after run completion.

      • Declog step removed from maintenance wash: The declog step introduced in a previous release has been removed from the maintenance wash recipe. This step was found to accelerate syringe wear beyond expected levels, and its removal restores expected syringe longevity.

      Known Issues, v3.4.3:

      • 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.

       

       

      AVITI OS v3.4.2

      Please Note: AOS 3.4.2 is a required release that must be installed before all future instrument software updates. The user may decide when to apply this update.

      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.

      For systems with slower network connections and upgrading from AOS 2.x, the AOS 3.4.2 upgrade may take between 1-2 hours to complete. If the upgrade process does not complete within 3 hours, please contact ElemBio Support at support@elembio.com. 

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

      • Sequencing Improvements
        • Stricter validation for filter masks and advanced settings: Ensures runs start with correct configuration.
        • Support for long reads in R1: Fixed an issue preventing >500 cycles in Read 1 for 2x300 kits.
        • Compatibility fix for Trinity Third Party workflows:  Corrected an issue that incorrectly required a minimum of 4 cycles for Index 1 when using 2×75 kits.
      • UI stability improvement: Corrected a rare condition that could briefly result in a “black screen” before the UI recovered.
      • Offline log export reliability improved: Fixed an issue where limited offline logs could not be exported when automatic offline log export was turned on.
      • New high-pressure alert during maintenance wash: The system now notifies you if high pressure is detected during a maintenance wash, indicating that additional maintenance may be needed.
      • Declog included in maintenance wash: The declog step is now automatically run as part of the bleach wash section of the maintenance wash cycle. (See Recipe Changes below)
      • Improved wash performance: General performance enhancements have been made to all washes. (See Recipe Changes below) 

      AVITI24-Specific Enhancements

      • Disk space alert threshold updated: Adjusted low-disk warnings to better support 2D sequencing runs.
      • Improved run robustness: Addressed an issue where hardware malfunctions errors occur, causing unexpected run interruptions.
      • CytoProfiling UI update: Tooltips for Small Cell and Expanded Z settings have been updated for clarity.

      Recipe Changes

      • Maintenance wash now includes declog: Declog is now automatically performed as part of the bleach wash step.

      Known Issues, v3.4.2:

      • If the upgrade from AOS v3.2.0 to v3.4.0 or higher takes longer than 2 hours, users should contact support@elembio.com.
      • In rare cases, if the firmware update does not complete successfully, the system may not initialize properly after a power cycle.
      • 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.
      • If the CytoProfiling flow cell leak test fails, users may be unable to discard their run, causing the UI to hang.

       

       

      AVITI OS v3.4.1

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

      • Fixes and Improvements
        • System Reliability
          • Resolved an issue in which a rare condition could cause the shutdown dialog to appear repeatedly following an instrument update.
        • Trinity™ Third-Party Support
          • Removed the xGen Exome Kit from Trinity Third-Party workflows (not supported).
          • Removed the Trinity short-insert recipe from Trinity Third-Party workflows (not supported).
          • Both options remain available for Trinity Elevate workflows.
        • Trinity Support
          • Updated Trinity recipe(s) to implement a 65 °C library hybridization step (previously 60 °C).
      AVITI24 Performance
      • Addressed rare issues where data processing could stall during AVITI24 sequencing runs.

      Known Issues, v3.4.1:

      • If the upgrade from AOS v3.2.0 to v3.4.0 takes longer than 2 hours, users should contact support@elembio.com.
      • 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.

       

       

      AVITI OS v3.4.0

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

      • Third-Party Workflow Integration:
        • Added support for distinguishing between third party and Elevate workflows within the Trinity™ user interface. Please note: Trinity products supporting third party workflows will be made available in a future release.
      • Polony Map Generation (PMG) Shift Enhancements:
        • Added PMG shift support for Trinity third party runs.
        • New PMG shift warning alerts users when no indexing is used, indicating that no data will be generated for skipped cycles.
      • Metric Display Fixes:
        • Resolved an issue where the Percent Passing Filter metric was displayed prematurely, prior to final calculation completion.
        • Fixed a bug where “NaN%” was shown for the Q30 percentage of Library Pool 2 during dual-library runs. The metric will now correctly display a placeholder (e.g., “–”) until actual values are available.
        • Resolved issue where the Reads metric was duplicated across library pools in Individually Addressable Lane runs.

      Applies to AVITI and AVITI24

      • Custom Recipe Support: Enabled compatibility with the Custom Recipes advanced run setting for Cloudbreak UltraQ™ workflows.

      Enhancements available today

      • Increased Sequencing Output:
        • Users can expect up to a 50% increase in reads passing filter when loading at higher concentrations with Cloudbreak™ and Cloudbreak Freestyle™ 2x150 and 2x75 kits. For more information on sequencing kit specifications on AVITI24, please see our website.
        • Users can also expect increased output with Trinity Sequencing kits with no change to loading concentration, allowing for up to 36 exomes per flow cell.
      • Advanced Setting – High-Density Polony Mode (Expert Mode HD):
        • HD Mode is now available exclusively for 2x300 kits. For 2x150, 2x75, and Trinity kits, current computational advancements implemented in AOS v3.4.0 deliver maximum achievable read output at this time.
      • Maintenance Wash Lockout Policy Update:
        • For AVITI24 instruments not running CytoProfiling workflows, the wash lockout period is extended to 30 days. Users must continue performing weekly maintenance washes, as per best practices.
        • If a maintenance wash is not completed within 30 days, the system will prevent new runs until a wash is performed.
        • Note: Once a CytoProfiling run is initiated on either side of the instrument, the wash lockout will automatically revert to 7 days.
      • Image Processing Fix: Resolved an issue where z-slices of Cell Paint tiles were intermittently missing during CytoProfiling runs, leading to faint projected images.

      CytoProfiling Enhancements (for products coming soon)

      Please note: products associated with the following software enhancements will be available at a later date.

      • Teton Focus Panels: Introduces pre-configured panels for custom protein batches in Teton runs. Available panels include:
      • Cytokine Signaling
      • T-Cell Activation
      • Innate Immunity
      • Cell Metabolism
      • Cell Stress & Apoptosis
      • Gene Regulation
      • Neurodegeneration
      • Neurodevelopment
      • Neuroinflammation
      • Teton Antibody Screening Kit: Enables antibody screening for custom protein batches. Supports the following configurations:
      • Cell Paint alone
      • Cell Paint + Control antibodies
      • Cell Paint + Control antibodies + Custom Antibodies
      • 48-Well Consumable Support: New consumable format compatible with all Teton Runs, Focus Panels, Teton Atlas, and antibody screening workflows.
      • ElemBio™ Cloud Integration: Planned runs now support 48-well consumables. All cytoprofiling workflows support custom recipes.
      • Teton Atlas Low Output Kit Support: Adds compatibility with the Teton Atlas Direct In-Sample Sequencing Low Output Kit, including onboard cell assignment using guide sequences.

      Known Issues, v3.4.0:

      • If the upgrade from AOS v3.2.0 to v3.4.0 takes longer than 2 hours, users should contact support@elembio.com.
      • 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.