Accessing Reference Photodiode Raw Values

Hardware, PWM, and Optics
1

Hello!
I am working on OD calibrations for the v1.5 pioreactor (40 mL).

I am interested in seeing the reference photodiode values (specifically the raw voltage signal) that are measured during this calibration. In a previous post (OD data management) it was mentioned that the command line could be used to see the values from an experiment. Is there a way to access this data for a specific calibration?

Thank you!

2

Hi @apemaraj,

If the calibration has been created already, the REF PD values aren’t available anymore.

If you can create the calibration again, try adding DEBUG=1 pio calibrations run ... to see more data for the reference PD.

3

Thanks! I just tried that and there doesn’t seem to be anything new showing up on the graphs. Will the values show up at the end of the calibration or is there something specific I should be looking for?

Another quick question, after running an experiment will the REF PD values show up in the UI? I remember seeing that it was a planned feature and wanted to check the current status.

4

Oops, right, this solution won’t work. Hm, I guess there isn’t a method currently. I am working on the OD calibration software now, and can think about how to add this. Can I ask what you are trying to do with the REF values?

Another quick question, after running an experiment will the REF PD values show up in the UI? I remember seeing that it was a planned feature and wanted to check the current status.

This is a good idea, you can do this infact, however it’s going to show the relative intensity, not the raw voltage. Here’s how to do it:

  1. SSH into your leader Pioreactor
  2. enter the following:
    nano .pioreactor/ui/charts/relative_intensity_of_ir.yaml
  3. Copy and paste the code in rel_intensity_ir.yaml · GitHub
  4. Save and exit with ctrl-x
  5. In your configuration, add the line
    relative_ir_led_intensity=1
    under section [ui.overview.charts]
  6. Save the config, and refresh the Overview page.
5

  1. I and a few others are working on trying to use the pioreactors to grow high density cell cultures. We wanted to use the raw voltage signal from the REF and the 90 degree photodiode and make our own calibration curve to better fit the OD range we are using.

  2. Thanks for that information! Is there any way to see the raw voltage of the reference diode?

6
  1. We have some updates coming out that will extend the OD range. I’ll DM you.
  2. Currently, the only way is to turn off using the REF as a reference. In your config.ini, find [od_config.photodiode_channel], and change the “REF” to “90”, for example:
[od_config.photodiode_channel]
# Default IR photodiode channel(s) to use and its angle relative to the IR LED(s),
# OR choose the reference photodiode using the keyword REF.
# Only valid angles are {45, 90, 135, 180}
# Only allowable channels are {1, 2, 3, 4}
1=90
2=90

Then when you start OD reading, you will see two lines, one for each sensor. Note that you can’t create or use calibrations if you do this!

7

Interesting thanks!
Is it possible to use channel 1 for the 90 degree PD and channel 2 for the 135 degree PD without a reference?

8

Yup, just change the position of the PDs, and use [od_config.photodiode_channel] to explain what positions the PDs are in.

9

Thanks for all your help! Just a quick clarification, I have changed the config file to 1=90 and 2=90. The data is plotting on the “Optical Density” plot. Are the Y axis values the voltage readings in V?

10

Yes, they are