hello—
very much a noob here, but I am struggling to make sense of the OD readings I am receiving. Pretty much all experiments I run, regardless of the visual appearance of the mixture, report a very low OD reading (around 0.02, never higher than 0.1). I placed black coffee into the vial to try and trigger a high OD reading and it outputted an OD of 0.01. And then I placed water in the vial and it showed 0.06. Any thoughts on what might be causing this? A hardware issue perhaps?
Thank you 
Or software - do you have a Pioreactor 20ml version 1.1 ? And which software version are you using (Available under “Inventory” in the UI)?
its a 20ml 1.0, using software 24.5.13
Hm, that’s strange. I don’t know the turbidity of your black coffee, but you may have hit the linearity limit and gone over into the decreasing signal territory.
Have you run a self-test on the Pioreactor? Running a self-test | Pioreactor Docs
Thanks for the reply. I just ran two self tests, results attached here. After the first test failed on the magnitude test I switched the IR led setting from auto to 25 to see if that did anything. On the second test the “photodiodes are responsive” test failed. checked the config and all seems ok, also didn’t change anything between the two tests other than reducing the IR led value and double checking hardware connections.
(Let’s ignore the “Photodiodes are responsive to IR LED” error)
The REF does seem really high… note that in the OD readings job, the final signal looks like:
[90deg signal] / [REF signal]
So if the denominator is big, then it will make the entire value small (as you’re seeing). Hm, can you check to make sure the IR LED is pressed completely into its pocket?
Also, another consequence of a high REF: the ir_led_intensity=auto will set the IR LED intensity to a value s.t. [REF] = 0.1, which in your case, is likely very low, so you may not be getting much signal in the [90deg signal].
Ok thank you Cam, I will try these and let you know!
Hi @lotusblood,
Did you manage to resolve that issue, I am running into the same problem with one pio in my cluster.
Best,
Arthur
Hi @ArthurV, which version of the software is that Pioreactor on? Does your self-test report back any failures?
Hi @CamDavidsonPilon,
I am on version 25.4.11, same as the rest of the cluster. The self-test reports 2 errors, the same as above:
I checked the connections, reassembled everything, cleaned the diodes/vials, made sure the IR and 90° holes were correctly 3D printed.
The ir_led_intensity is set to 70 in the config file, with the rest of the parameter being as they should.
The only problem I just noticed is that the voltage on PWM rail on this pio specifically is capped to 0.1 V whereas the other are around 5V, adding the external power supply (12V) doesn’t help. Could that be a sign that the raspberry is fried ?
The only problem I just noticed is that the voltage on PWM rail on this pio specifically is capped to 0.1 V
Hm, where are you seeing that? (That is, how are you measuring this?)
Hm, right, that’s may be a symptom of another problem. There is a connection between that number (voltage) and ADCs, mentioned here: When the PDs are saturated, the other ADC readings are wrong · Issue #452 · Pioreactor/pioreactor · GitHub
Can we simply the setup: remove any AUX power attached, power-cycle the unit, and see if both problems persist?
