Offline OD calibration

Software
1

Hi Community,

I was trying to calibrate the OD600 in Pioreactor and wonder if there a way that I could do offline calibration offline and insert the correlation coefficient into the software?

Thanks a lot.
Supiwat

2

Hi @Supiwat,

You kinda can! The output of the calibration is a json blob. and the important part of that the fields curve_data_, which represents the calibration polynomial’s coefficients (x=OD600s, y=pioreactor signal). In your case, it’s a linear curve with leading coefficient equal to the covariance (not correlation) and an intercept term. Note that you do need the covariance and not correlation, as the former has the required information.

We are currently re-thinking how users interact and create calibrations, but here is I think the easiest way to add your offline:

  1. In your config.ini, confirm that ir_led_intensity is not auto. This is true for all od_calibrations.
  2. SSH into the Pioreactor you wish to modify:
  3. type python3 to open up a Python shell.
  4. copy-and-paste the following, but where I have ALL_CAPS, put in your information instead:
from pioreactor.actions.od_calibration import save_results
unit_name=THE_PIOREACTOR_NAME
calibration_name=A_UNIQUE_CALIBRATION_NAME
covariance=COVARIANCE
intercept=INTERCEPT
save_results([covariance, intercept], 'poly', [0], [0], "90", calibration_name, "2", unit_name)
  1. You should see a message like
    Set `my-offline-calibration` to current calibration  ✅
  2. Exit the shell by entering exit().

You probably have more questions, so I’m happy to help further!

3

Is there a way to copy the calibration from one pump to another to get up and running quickly? I calibrated my media pumps and see the cache.db but its jiberish to me.

I’ve already started a run and I can’t turn on turbidostat dosing because my waste pumps aren’t calibrated, but their calibration is not critical since they can run long and the total volume controlled by the waste outlet level.

4

Hi @DocRuzzy, yea, there’s an easier way if your goal is just that (and we plan on making this even easier later).

  1. SSH into your Pioreactor
  2. run pio run pump_calibration display
  3. Find the part between { and }. Copy all that to your clipboard.
  4. Open a new file with nano pump_cal.json, and paste the results into this editor. Save and exit with ctrl-x.
  5. Finally, run pio run pump_calibration -f ~/pump_cal.json and follow the promps (eg: choose waste, give it some name, etc)
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