Hello!
We recently updated our software to version 24.10.1. Since then, we are getting recurring warnings about the REF photodiode on various units:
The reference PD is very noisy, std=0.012. Is the PD in channel 1 correctly positioned? Is the IR LED behaving as expected?
We also noticed that the OD readings have become much more noisy since the software update. I suppose that these could be related issues.
Example of experiment before update:
Example of experiment after update:
Would you have any idea what could cause this?
Best regards,
Mandy
Hi @mandy-twig,
Hm, what version were you on before? Are your Pioreactors OD600 calibrated?
Hi Cameron,
We were on version 24.9.19 previously. The OD600 is calibrated for all units. I did not change the calibration between these experiments.
I think this is resolved in the next version, 24.10.28. I would try that first.
Okay, thanks I update the software to the latest version!
Another dataset to look at is “IR LED intensities” from Export data page in the UI. This is a timeseries of what the REF is recording. If you see large dips in that signal, then I would expect something strange is going on with the IR LED (and not a optical / calibration problem).
I had a look at the IR LED intensities of past experiments, and it doesn’t look very stable. I don’t know how much noise you would expect. What do you think?
Another issue that might be related is that our lab is only air conditioned during working hours. This has a strong effect on the temperature readings, which are much more noisy when the air con is on. We changed some temperature config settings in, so the effect of temperature is less in exp2.
exp1 (air con off between 3 and 15 hours)
exp2 (air con off between 9 and 21 hours)
Okay interesting!
IR and OD from Twig-pio-0008 (first figure) looks about right: the IR intensity will vary will temperature, and we are seeing that here (AC triggering on/off cycles, and then completely off). The magnitude of the changes seem correct too (quite small). FYI We normalize the OD by this signal, so temperature effects in the OD are reduced.
However, in IR and OD twig-pio-0016 (third figure), the signal looks incorrect! There’s too much noise in the REF, and that’s why you’re seeing the warning about “REF variance too high”.
Since it’s happening to all your workers, it’s clearly some software issue and not hardware. I suspect it has to do with triggering the IR LED. Try upgrading, and see if that solves the issue. We can also investigate at your plugins to see if they might be interfering, too.
We have now updated our array to the latest software. I will inspect the IR data after the next experiment and get back to you when the issues does not seem to be resolved.
Thanks for your quick replies!
