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      AVITI™ OS 3.4.0, 3.4.1, 3.4.2 Release Notes

      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. 

      Summary of Changes

      AVITI OS v3.4.2

      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.