Blanking the OD

1

The button “blank” in the OD blanking menu (under calibrate) is in gray and I can’t press it.
How can I make it work?

2

There are some bugs in the UI dialog box (that will be fixed in the next software release, this week) - try refreshing the page. If that still doesn’t work, try SSHing into the Pioreactor and manually running it with pio run od_blank

3

thank you for the answer.
Now the “blank” button isn’t in gray and it does respond with a “loading” symbol, but after a few seconds it turns off and nothing happens.
When I tried running what you suggested manually, here is the prompt I received:
“RuntimeError: od_reading is already running. Skipping”
should i do this before I activate the OD? but then how will the app know what OD is the blank value?

4

Ah yes you should do this before OD reading. Here’s the sequence:

  1. Prepare a blank vial, and put into the Pioreactor.
  2. Run OD Blank from the UI. When it’s finished, it stores the data on the Pioreactor’s SD card per experiment
  3. When you run OD reading next, it will look for an OD blank from that experiment.
5

Thank you Cameron.

I am still unsure about the normalized OD.
Although I get a similar stationary-OD of 0.8 between different experiments, the normalized OD can vary between 60 to 400 and it’s harder to find a pattern.

6

Hm, if you’re seeing that much variation, it sound like the initial delta (reference_od - od_blank) is very small (see here) and any noise here is causing large deviations.

A simple way to solve this is to add more culture initially. And if you do that, you can perhaps also skip the blanking process since reference_od >> od_blank.