So the highlighted jumps are expected. If you move the REF, it changes the normalization that occurs in the OD readings:
raw OD reading = [90deg signal] / [REF signal]
So any disturbance of the REF signal will shift the OD reading.
The other jumps appear too unnatural to be biological. I wonder - are the REF photodiodes under some tension, and shifting suddenly to a new position at some point throughout the experiment?
(Internally, we’ve used that blue sticky tac to hold a PD and LED cap in place - a better solution to PDs is coming in the future)
However, this would show up a big jump in the dataset ir_led_intensities. You can confirm you see a jump in that dataset at the 24h mark (the highlighted jumps)
Other ideas / information:
- The IR LED intensity is static throughout the experiment. Even if it changed, then it would affect [90deg signal] and [REF signal] about the same, hence the ratio [90deg signal] / [REF signal] wouldn’t change (that’s the idea!). So I don’t think
ir_led_intensityis the problem. - If the problem isn’t [REF signal], what might cause [90deg signal] to increase? Do any jobs start or change at the same times? Like does stirring’s RPM increase or decrease, and other LEDs come on, etc.?
- Are these near a window, and lots of ambient light suddenly hits the Pioreactor?