1. Resources
  2. Here

AVITI OS 3.0.0, 3.1.0 Release Notes

Please Note: For systems with slower network connections, the AOS 3.1.0 upgrade may take between 1-2 hours to complete. We recommend users initiate the update during a period of instrument downtime. During the update process, the system may restart multiple times as part of the upgrade procedure. If the upgrade process does not complete within 3 hours, please contact ElemBio Support at support@elembio.com.

Summary of Changes

AVITI OS v3.1.0

For AVITI24™ instruments, support for Teton™ CytoProfiling kits and flow cells:

  • Maintenance wash is now required on AVITI24 instruments after 7 days


Sustaining Improvements:

  • Added support for AVITI 2x75 Sequencing Kit Cloudbreak Freestyle, Low Output, PN# 860-00034
  • Introduced a new Advanced Run Settings add-on for PMG Shift, allowing AVITI OS to defer polony map generation to later cycles when early cycles show low diversity.


General Bug Fixes:

  • Resolved an issue in AOS 3.0.0 affecting the Standard Sequencing Recipe, where the polony filter was unintentionally relaxed when runs were configured via the instrument UI.
  • Resolved an issue in the Element Short Insert Recipe by updating the amplification temperature to the correct value
  • Improved instrument robustness to primary analysis edge cases


v3.1.0 Known Issues:

  • If leak errors are triggered for both sides of the instrument, AVITI OS cannot unlock the waste module door.
  • If the AFIC board loses power, it does not restart automatically and requires a power cycle. If the instrument experiences a power interruption or loss, power cycle it once through the UI after power to the instrument is restored.
  • The run can continue even if polony map generation fails, as AVITI OS cannot detect a particular failure scenario.

AVITI OS v3.0.0

For AVITI24™ instruments, support for Teton™ CytoProfiling kits and flow cells:

  • Introduced a new Teton CytoProfiling run setup option with accompanying updates, including enhancements to disk space checks, run manifest parsing, flow cell scanning, and consumables validation.
  • Added custom recipe support for Teton CytoProfiling runs.
  • Enabled support for Teton™ CytoProfiling runs planned through ElemBio™ Cloud.
  • Introduced new flow cell leak and leak recovery tests specific to Teton CytoProfiling runs.
  • Implemented a new run type for executing Teton CytoProfiling recipes.
  • Added the following metrics and charts for Teton CytoProfiling:
    • Target Expression Metrics: Heat map displaying target expression levels in each batch relative to other wells.
    • Assignment Rate: Bar chart showing the percentage of polonies successfully mapped to a target, including percentages of exact matches and near matches (1–2 base mismatches).
    • Quality Controls: Bar chart showing the average count of quality control targets per cell in each batch.
    • Thumbnails: Stitched image overlay of cell membrane and nuclear cell paint targets for a quick view of cell culture and fixation success.
    • Run Configuration: Displays details such as kit, well layout, and storage location.
    • Cell Count: Total cells segmented in the run.
    • Cell Confluency: Percentage of flow cell area covered by cells.
    • % Assigned: Percentage of polonies successfully mapped to targets across all batches.
  • Teton CytoProfiling run output includes additional files, such as cell paint projection files, assigned polony locations, and cell statistics.
  • Added support for flexible start configurations with sequencing assays, including 12-well and 1-well single-sided, dual-sided, and flexible options. Running a dual-start configuration with a single well is not recommended at this time due to performance limitations that can cause disk overfill and run pauses.


For AVITI and AVITI24 instruments, support for Trinity™ sequencing:

  • Added support for Trinity onboard enrichment in the sequencing workflow, including the following components:
    • New Sequencing Kits: Trinity 2x75 and Trinity 2x150
    • New Trinity Flow Cell
  • Added Trinity panel options for Twist, IDT, and Other. When a Twist or IDT panel is selected, AVITI OS writes the associated BED file to the run output folder for secondary analysis.
  • Enabled flexible start support for Trinity runs, allowing a run on one side to pause and a new run to start on the other side.
  • Enabled support for Trinity sequencing runs planned through ElemBio Cloud.
  • Introduced a short insert custom recipe specific to Trinity, available in Advanced Run Settings.
  • To analyze Trinity data, ensure Bases2Fastq is updated to version 2.1.0 or later. For details, refer to Version Compatibility in the Online Help.


Sustaining Improvements:

  • Made Advanced Run Settings for Expert Mode (Polony Density) and Custom Recipes (short and long insert options) available to all customers without requiring add-ons.
  • Updated the display names for Cloudbreak Freestyle™ sequencing kits and flow cells to CB Freestyle to align with packaging.
  • Moved the planned run selection to the Run Setup screen, enabling users to toggle between planned and manual setup modes.
  • Added an SMB storage connection setting for File Checksums. When enabled, the software generates and stores MD5 checksums for each file created and transferred in a sequencing run within the RunUploaded.json file.
  • Removed support for obsolete Version 1 chemistry sequencing kits and flow cell.
  • Resolved an issue in AVITI OS 2.5.0 and earlier versions for online instruments, where the software failed to recognize a single local storage connection as the default if cloud connections could not be verified. This previously prevented wash runs from proceeding.
  • Resolved a previous issue to ensure that offline instruments can complete full log exports.
  • Increased the SMB Timeout from 10 seconds to 90 seconds to improve upload reliability for instruments with slower internet connections.
  • Changed UID generation to originate from AVITI OS.
  • Upgraded the base image to version 3.0.0.


v3.0.0 Known Issues:

  • If leak errors are triggered for both sides of the instrument, AVITI OS cannot unlock the waste module door.
  • If the AFIC board loses power, it does not restart automatically and requires a power cycle. If the instrument experiences a power interruption or loss, power cycle it once through the UI after power to the instrument is restored.
  • The run can continue even if polony map generation fails, as AVITI OS cannot detect a particular failure scenario.
  • The Element Short Insert Recipe includes an incorrect amplification temperature when runs are set up through the instrument UI. However, this issue does not occur for customers using the ElemBio Cloud Planned Runs feature, where the correct settings are applied. For customers operating offline or not utilizing ElemBio Cloud Planned Runs, please contact support@elembio.com to request a custom, corrected recipe file, or update software to AOS3.1.0.
  • In AOS v3.0.0, The Element Standard Sequencing Recipe includes a relaxed polony filter when runs are set up through the instrument UI. However, this issue does not occur for customers using the ElemBio Cloud Planned Runs feature, where the correct settings are applied. For customers operating offline or not utilizing ElemBio Cloud Planned Runs, please contact support@elembio.com to request a custom, corrected recipe file, or update software to AOS3.1.0.