AVITI™ OS 3.4.0, 3.4.1 Release Notes

Please Note: 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 3.4.1 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 v3.4.1

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.