Release Note: CODI & CODI System App

Release Note: CODI & CODI System App

July 2025 Update with CSA 1.0.21

July 28, 2025

This release contains big updates across CODI!
  1. We’re rolling out support for AutoLNP on Aplo Scope, enabling 3x more data from your LNP Profiler kit to be acquired thanks to the large, homogeneous field of view.
  2. We’ve unified our help desk links, including those to the help desk and individual tools such as analysis tools. Make sure to update your bookmarks to the Ticket Submission page
  3. For all acquisition apps (AutoEV, AutoLNP, and Aplo Scope Control):
    1. Improved the connection between CSA and the CODI webpage, which should improve the reliability of the camera stream.
    2. [Aplo Scope] CODI System App (v1.0.21 onwards) now remembers your previous system heating settings and will automatically start heating to the target temperature when you start CSA.
    3. [Nanoimager] "Nanoimager Info" page renamed to "System Info" page
  4. For Aplo Scope Control:
    1. We’re introducing custom Workspaces in Aplo Scope Control, allowing users to save and load their illumination and multi-acquisition settings. This is a great way to quickly set up acquisitions with consistent channel names and imaging sequences!
    2. The TIRF angle will now be retained when switching between CODI tabs.
    3. Channel mapping now includes automatic laser power optimisation which finds the best laser power for each channel independently.
  5. For AutoEV and AutoLNP:
    1. [Nanoimager and Aplo Scope] Improvements to the autofocus algorithm should reduce the need to refine focus in each lane.
    2. Bug fix:
      1. Fixed legend labels are corrected in the EV and LNP report
  6. For AutoLNP: 
    1. We’re bringing AutoLNP to Aplo Scope with this release, including some great new features and Aplo Scope-specific updates
      1. A redesigned Acquisition screen puts the large field of view front and center and re-organizes the widgets to allow you to focus on your LNPs
      2. A new “Optimize Lasers” button in the Channel Mapping microscope controls automatically sets the optimal laser power in % for your experiment, based on the known power densities required for the LNP Profiler kit.
    2. Bug fixes and improvements for Nanoimager and Aplo Scope:
      1. Improved background corrected Cargo image channel on CODI to prevent misleading dark features at low intensity
      2. Fixed LNP Clustering failure in CODI with large (~1.3 M locs) localization density per channel 

June 2025 - AutoLNP and AutoEV Updates with CSA 1.0.3

June 02, 2025

This release contains updates for our acquisition apps:
  1. For all acquisition apps (AutoEV, AutoLNP, and Aplo Scope Control):
    1. Bug fix: Fixed issues related to camera stream display
  2. For AutoEV and AutoLNP:
    1. New CSA v1.0.3 for both AutoEV and AutoLNP apps
    2. mW power reader for single laser power in AutoLNP and AutoEV 
      1. In the microscope control laser widget you will now have the laser power reported in % and mW. It reads one laser at the time. 
  3. For AutoLNP: 
    1. Cargo channel with background correction visually displayed in CODI!
      1. The AI LNP Profiling, in the positivity step, will show you the cargo channel with background correction as default (previously it was visually still the raw image). You can switch between background correct and raw at any time and compare the two images. 
        1. Default is now diffraction limited channel with background correction applied 
        2. It is always possible to change it to raw diffraction limited 
    2. Bug fixes:
      1. Inconsistency of header naming in csv file for the positivity groups 
  4. For AutoEV:
    1. Ability to skip FOV during an acquisition 

September 2024 - Aplo Flow EV Prep Phase 2 Release with CSA 0.19.5

September 25, 2024

This release contains the Phase 2 update to the Aplo Flow EV Prep app:
  1. Support for the PanEV reagent
  2. Completely overhauled UI/UX with significant "quality of life" improvements:
    1. Save channels and sample details
    2. Pause/abort
    3. Error status reporting
    4. Door lid status reporting
    5. Drag-n-drop interface for plate/sample setup
    6. 1-to-many relationship for reagents and samples
  3. Numerous bug fixes

August 2024 - AutoEV August 2024 Release with CSA 0.18.25

August 12, 2024
  1. System warnings about temperature and channel mapping now have a “do not show again” button. These warnings provide important information to ensure that autoEV acquires data reliably and accurately, and we recommend using the “do not show again” buttons only for expert users who are familiar with the nanoimager’s thermal and spectral stability over time. To reset these warnings, you must reset your browser cache or delete your browser’s local storage.
  2. When a new collaboration is created from AutoEV’s experiment setup screen, it will now be selected by default
  3. The experiment settings that are currently loaded are now displayed prominently
  4. Regenerating AutoEV Reports
    1. When using the Cross Dataset Report function from a collaboration’s batch download page, if the selected analysis app is EV Profiling, it will use the new AutoEV report style
    2. Customers can also generate a report with different analysis settings, or combining datasets from several autoEV uses.
  5. Bug Fixes
    1. Fixed an issue where the CODI browser would lose connection with the CODI system app, and the user would have to click “refresh” several times to re-connect.
    2. Fixed an issue where the CODI browser erroneously displayed the “exclamation mark” in the nanoimager info icon, indicating that the CODI system app was disconnected, even while it was actually connected
    3. Fixed an issue where the camera stream would not appear, or would take several seconds to appear. The camera stream should now appear consistently.
    4. Fixed an issue where System Calibration would fail during AutoTIRF optimization on certain systems where the TIRF angle optimization would attempt to increase past 60°.  This now respects the value in the instrument data file under the key:  hardware -> illumAngleStage -> upperLim

Initial AutoEV Release with CSA 0.18.4

AutoEV is a workflow built for EV researchers. From the moment you place a chip on the Nanoimager, all steps to ensure optimal imaging conditions and settings are staged in a simple-to-follow interface and done for you, even eliminating finding and setting focus and optimal TIRF angles for imaging. AutoEV automatically pushes the data through to analysis, generating data on sizing, clustering, and positivity, shown in real-time, resulting in a beautiful one-page EV-focused report automatically generated after the run is complete.

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