AutoEV and AutoLNP Troubleshooting

AutoEV and AutoLNP Troubleshooting

Updating CODI System App (CSA)

When prompted to update the CODI System app, it is critical that the update is performed before running an experiment. This update message appears when the CODI website has been updated but the CSA version on the machine is older than the version required for the website.
Alert
Running an AutoEV or AutoLNP experiment without updating to the requested CSA may result in data loss or incorrectly acquired data.

Refresh page message

Sometimes a popup message asking to refresh the page may appear. This can be due to CSA not being connected properly. Click the "refresh" button to attempt to restore the connection. If refreshed when inside the AutoEV or autoLNP page, any status or data will not be lost.

"Could not connect to CODI System App" message

A popup message may appear asking to refresh the page will appear. This can be due to CSA not being connected properly. If refreshed when inside the AutoEV page, any status or data will not be lost. If refreshed while navigating in CODI analysis (any CODI tab that is not the AutoEV app), the AutoEV app tab will disappear. Do not worry!
Simply go back and everything will be restored.

Calibration or Refine Focus Failing

Note: Calibration may fail for several reasons. Errors will appear in the top right corner indicating the reason for failure. Common sources of failure are inability to find the lane surface or find the optimal focus based on the fluorescence signal due to too few points being detected. If the system calibration fails consistently or autoTIRF looks poor, follow these instructions: 
  1. First, ensure the Assay Chip is properly positioned on the Nanoimager stage, and that the lanes are bubble free. Note: If the failure appears to be focus related, select the Refresh z-lock calibration option.
  2. Next, try a different channel or lane where a strong signal is expected and then re-run the calibration by clicking Calibration failed. Re-calibrate focus & illumination. AutoEV will move to the next FOV and try again. This means if the area was bleached, or bad, or if oil was not well distributed, there is a chance to succeed by moving to a different area. 
  3. Verify that the system is not attempting to calibrate in a zone where there is a bubble in the chip. This can be visually inspected by opening the Nanoimager lid after a failed calibration and observing the sample from directly above the objective. If there is a bubble, try calibrating in another lane.
  4. If the system fails to focus, it could be attempting to focus on the wrong surface of the chip. Set the global settings in the System Info page to ensure best focus.
  5. If the system focuses but fails to optimize the illumination angle, the sample could be bleaching before the optimization completes. Lower the laser power for the system calibration in the System Info page to prevent bleaching.

Laser error while running System Calibration, Sample Pre-check or Acquiring Data

AutoEV and AutoLNP perform a number of system performance checks to ensure that data will be acquired accurately and consistently. Some of these checks verify that the lasers are able to reach the specified power in a reasonable time. If the lasers are unable to operate to desired performance, follow these troubleshooting steps:
  1. Submit a ticket to let your ONI support representative know you're having laser issues. Be sure to include your system logs with your ticket (See section below)
  2. Change the target laser power:
    1. For System Calibration, the laser power can be modified in the System Info page. For example, if the system is having difficulty setting the 561nm laser to 5%, change the "561 laser power for calibration" value to a slightly higher value, like 7%.
    2. For Sample Pre-Check or Acquisition, the laser power is modified in the Experiment Setup page, on a per-lane basis.
  3. Close the CODI System app, and power cycle the Light Engine attached to your Nanoimager or Aplo Scope by flipping the power switch off, waiting 5-10 seconds, and flipping it back on. Wait ~30 seconds for the light engine to power up, and then re-open the CODI system app.
  4. If automated System Calibration continues to report laser issues, use Manual System Calibration to manually set the illumination angle and per-lane focus for your experiment.

Setup AutoEV or AutoLNP in a new browser or browser profile

The global Acquisition Settings in the System Info page provide initial values for AutoEV and AutoLNP's automated algorithms like 1-click channel mapping, system calibration, autofocus and autoTIRF. Having proper values is critical for ensuring these automated algorithms function correctly.

These initial values are stored locally inside the web browser profile used for AutoEV or AutoLNP. If the browsing data is deleted, or a new user profile or web browser is used to access autoEV or autoLNP, these settings will need to be reset. The following table provides guidance on suggested initial values for Nanoimager or Aplo Scope.

Setting
Nanoimager Suggested Value
Aplo Scope Suggested Value
Starting focus for channel mapping
0
0
Starting focus for system calibration
-250
-250
Manual TIRF angle
54
60
488 laser power for system calibration
15*
5*
561 laser power for system calibration
15*
5*
638/640 laser power for system calibration
15*
5*

* If not signal is detected when calibrating with the specified wavelength, increase the laser power for calibration
 

Submitting System Logs

System logs can be found here: C:\Users\ONI\AppData\Local\ONI\OHM, where "ONI" is the name of the Windows user account. If you are using a different account than the default ONI account, please note that the logs will be found in the same relative directory inside your active user account's folder.

When submitting logs to ONI for debugging, please:
  1. Sort the files in this folder by date to find the most recent logs
  2. Create a .zip file of the recent hal_*.log and experiment_server_*.log files from recent CSA runs. Note that each time CSA is opened, a new hal_*.log and experiment_server_*.log file are created
  3. Send that .zip file to ONI.

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