Problem with OD calibration

[david020506]

I tried the Control Computer as it comes from the LabMaker manufacture and it worked nicely to detected and start up the system, when running bash cb.sh. However, I am having trouble doing OD calibrationw. If I input “Actual” OD as 0, after introducing the “Measured” signal, the “Current” value (left to the “Actual” box) becomes zero and all ODs recorded during the experiment are always zero. If I input any “Actual” OD > 0 (e.g 0.5) then “Current” is set always to 100000 and the OD reported is not 0.5 but something larger (e.g 1.2). Although this number is not the real value (which should be 0.5), it does increase during the cultivation. In fact, it seems that the raw signal is correct but the conversion to OD is wrong. Any idea why this is happening and how to solve it?

Thanks a lot in advance!

[harrison]

Hi David,
Let me just confirm, what you are doing is the following:
1. Click measure.
2. Read a value of approximately 10000 from next to the word “Raw”
3. Copy this value (10000) into the box “New”
4. Put the actual OD (lets say 0) into “Actual”
5. Click “Set”
6. Current should now change to 10000.

From what I understand is step 6 not working for you? If the description of this process in the manual did not make sense (it sounds like perhaps you didnt copy the RAW value into the NEW box), then I can update it!
Good luck

[david020506]

Dear Harrison,

Thank you so much for taking the time to answer my question.

I do the following:

1. Click measure.
2. Read a value of 13271 from next to the word “Raw”
3. Copy this value (13271) into the box “Measured” which in right of the “Actual” Box. There is no “NEW” box, except for the one above the “Measure” box, which sets a Target OD for regulation.
4. Put the actual OD (lets say 0.01) into “Actual”. Here if I put 0,the current value always changes to 0.
5. Click “Set”
6. Current changes to 100000, not 13271 as expected. In fact, any value larger than 30 sets Current to 100000.

I started playing around with the value I introduce in the “Measured” box and found that for an “Actual” OD of 0.01,the “Measured” value should be something like 23 in order to make “Current” change to 13271. When doing this, measured values displayed in the OD chart during the experiment indeed start at 0.01 and increase to reasonable values during cultivation, although they don’t match the OD measured in our spectrometer.

Any suggestions are welcomed =) Thanks a lot again!

[harrison]

Hi David,
This is a very peculiar problem, and I am at a loss for how to explain it. Have you edited the Chi.Bio software in any way? It sounds like you are doing everything exactly correctly, so I am not sure how the numbers can get mixed up in the softrware. The 100,000 value arises because this is the maximum value you are meant to be allowed to set in that value – which seems consistent with your observation that any thing except very low inputs at “Measured” cause it to output very large values.

One way to diagnose would be to add extra print statements in app.py. Could you go into the function CalibrateOD and add the following just before the line that currently reads “sysData[M][item][‘target’]=OD0” (so, around line 1480)

print(‘ODActual = ‘ + str(ODActual))
print(‘raw = ‘ + str(raw))

And see what these numbers are showing you? (When you do the OD calibration it should display these lines in the Putty window).

[david020506]

Dear Harrison,

I had time to look again at this problem and it now works. I replaced the old app.py and cb.sh in my ChiBio (which came built-in in the device) for the current version of the files in https://github.com/HarrisonSteel/ChiBio. It seemed that the previous version of the app.py had some bug.

Thanks for your help!

Cheers

[Author]

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