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?
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
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?
Ah yes you should do this before OD reading. Here’s the sequence:
- Prepare a blank vial, and put into the Pioreactor.
- Run OD Blank from the UI. When it’s finished, it stores the data on the Pioreactor’s SD card per experiment
- When you run OD reading next, it will look for an OD blank from that experiment.
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.
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
.