Did anyone try the spectrometer-reading-plugin with the Adafruit AS7341 spectrometer sensor attached? In my experience, the OD readings after calibration are somewhat not supper reliable (I need quite excact readings for my experiements and had problems getting there in the past) and I am wondering if the OD readings with the plugin and attachement are reliable and if anyone already has some information about it.
Also, is it possible to read ODs at wavelenght 600 with that attachement?
A few users have mentioned that the spec readings aren’t great. It could be a hardware, code, or optics issue. I’ll spend some time this week investigating myself.
Can you share more details about the lack of reliability you are witnessing?
Well I tried calibrating all of my Pioreactors (i have a cluster of 5) and then running first experiments - for example just adding the same amount of saturated bacterial culture to media and add this to all of the vials - and i experienced quite great differences in OD readings even though they shoul all nearly do the same. I had some time off now and will restart the setting up and experiments with the Pioreactor, but in the end it would be great to have comparable and reliable OD readings between the Pioreactors in my cluster. Also, a question for that: When I do the calibration I use bacterial culture starting let’s say around 1.5 OD600 and I want to get down to 0.1, so I add LB Media the whole time and in the end I am being asked which my LB Media ODs is - I am always confused by that since in the lab here we work with LB as a blank (I will be only using LB for the Pioreactors) and I am wondering if I can also just use LB as my blank then so give the OB600 of 0 when I am asked for the OD of my Media or if i should blank my LB against water (and also all of my test measurements with the photometer here i am feeding the Pioreactor while calibrating) prior to calibration. Also then, when done calibrating and when i use this file with experiments, do i blank against LB then or not at the start of an experiment? I just want the OD of my bacterial culture of course… So but since there were big differences in between the readings I am looking for a better way of handling this.
Yes! That’s too be expected, and I apologize if you aren’t getting good concordance between the units. Are you able to share some of your calibrations here, or privately at email@example.com? To do so, SSH into a few different workers, and enter:
pio run od_calibration display
and paste here, or copy the output to a file and email me.
I believe the correct thing to do would be the latter: enter the OD600 measurement of LB against a true blank (water, or empty). However, I imagine the OD600 of LB is nearly 0, so you may be able to get away with entering 0.
Thinking about this: you would still perform the blank against LB using the Pioreactor’s built in routine. Note that this only affects the growth-rate calculations, and not the OD readings, so it doesn’t explain your differences.
However, you raise a point: is this needed to be done? The answer is no, since we have the blank data already (provided during the calibration), so our software should be able to provide this value automatically. We’ll implement that in the next version.