OD measurement issue - reactor insists the value is constantly 0.6

Hardware, PWM, and Optics
1

Hello pioreactor community!

I have a weird one for you. My pioreactor 20 mL v1.1 (software version 25.4.11) has been encountering a strange error for the past week.

The lab is located within a hospital campus, where there are monthly routine power shut-downs to test the backup energy supply. These power shutdowns can be problematic for any experiment we have that requires continuous power, such as our pioreactors. Last monday, there was a power shutdown that affected several experiments. The reactors lost power, and we had to resume the (turbidostat) experiment activity via the UI the following day.

Since the shutdown, there is a recurring error in one (but not all) of our reactors. Basically, the OD measurement will start reading at around 0.6 regardless of the actual optical density within the vial. After taking some culture out and measuring via cuvette this past friday, the culture measured 0.8.

To try and fix the issue, I stopped the experiment activity, rebooted the reactor, and ran a self-test. All tests passed, so the experiment resumed. The experiment continued running dilution cycles until about 10 am this morning, where again the OD measurement is stationary at 0.6 even though the actual value is higher.

I double checked that the correct OD calibration is active, which we made using standards of known OD values. I am additionally going to check the connection between the LEDs and the HAT and ensure that there are no visual defects with the LED and cables themselves.

I am not quite sure what to do other than that - last time it seemed that simple rebooting is enough to restore proper function temporarily. I will do this again, however these OD errors are not sustainable for a longterm experiment.

Has anyone else experienced these errors? Is it possible that the monthly power shut down damaged the HAT or other pioreactor hardware? How should I go about fixing this error?

Thanks for your help :slight_smile:

dylan

2

Hi Dylan,

So it starts at 0.6, but does it change over the course of the experiment? Is there any “noise” in the OD data, or is it pretty much a static value?

If running a turbidostat, and you get dilutions, it sounds like the OD is changing or 0.6 > OD set point and it just keeps trying to dilute.

Just a few ideas:

  • Can you check the value of smoothing_penalizer in your config? It should be ~6, and not ~700.
  • Can you SSH into the pioreactor, and show the result of pio version -v? Do you see firmware version 0.5? If on 0.4, this might be the problem.
3

Dear Cameron,

Thanks for the quick reply as always!

My smoothing_penalizer in my config.ini was indeed set to exactly 6.0, and the firmware version is 0.5.

Here is a screenshot of the UI to show the issue:

image
image1920×1080 244 KB

Basically the OD measurement has been accurate and reflective of real vial conditions until suddenly it isn’t, and the value reading is 0.6 with only a bit of noise. The measurements range from 0.61-0.59. Today I rebooted the reactor at around 15:30 local time and this fixed the issue again, however I worry that these fixes are only temporary.

Thanks again for your help!

dylan

4

hm, weird. Can you send me your logs dataset export for this experiment to cam@pioreactor.com?