[harrison]

It does seem suspicious that it would stop working then magically start up later. My best guess would therefore revert back to the moisture sensors – perhaps the one half-way down inside the device was tripped.
Or, it might indeed be a hardware issue, perhaps temperature changes etc helped it re-make a good connection. Hopefully it keeps operating as expected…

[harrison]

Alternatively you could measure the power supply with a multimeter to check if it is as expected.
Probably this is an unlikely cause – given it worked previously, it seems more likely that the reactor/hardware might have broken (probably there is a bad solder connection) rather than the 12V packing in.

[harrison]

Hi Lachlan,

I’ll assume everythign is plugged in and powered on etc.
Maybe one approach would be to try a different 12V power supply, and different USB cables in case they are broken somehow.

Failing that I would have to say the most likely application is a fault in the hardware/assembly which is somehow preventing it from communicating with the reactor. I don’t think moisture is the issue (as you said) since usually if that is the case it wouldn’t reach the “start up complete” message without error.

Unless you want to get in the device and start soldering connections etc probably the best approach is to reach out to labmaker and ask if they can replace/fix it.

[harrison]

That’s a very good question. It probably is a foundational problem with the Beaglebone chip that it has half an operating system on it – potentially preventing it from booting.
I do not know how in particular to fix it, perhaps there are other beaglebone users (unrelated to Chi.Bio) who have had the same problem online. If it isn’t taking a new flasher SD card then perhaps your only option is to buy a new beaglebone (they are not particularly expensive on their own)!

[harrison]

If you run with my second suggestion (using turning on the RegulateOD function) then those things wont be an issue – it shouldn’t overflow or reduce volume.

We do not have a dramatically more documented version, if you want to learn more best bet is looking at the comments, description in the Supplementary Information of the paper about the platform in PLOS Biology, and the user guide. Making more documentation has been on my to do list, but it never reaches a very high position by the time other items come to overtake it…

[harrison]

Something else occured to me as a potentially strategy: If instead of turning the PUMPS on every 12 hours, you might do better to turn on the OD Regulation function even 12 hours, and have it set to (for example) try to reduce the OD to half of whatever it’s value is at that time. Then, have it do a check that turns off the regulation once that target is reached. This way, the pumps will always provide an appropriate amount of liquid (i.e. in terms of factor of dilution), which you would not achieve by just setting them to a fixed flow rate for a fixed amount of time.

[harrison]

No worries.
One practical problem you may encounter would be that the pumps will need calibrating to make sure they are injecting the same amount of media as each other. Without this I would guess it might vary by up to 50% between pump heads, since the pumps used are the cheapest ones available!

[harrison]

I am afraid if it is going to be that infrequent you will need to do it in the python.
Probably the easiest way to do so would be to add a conditional statement in the main loop of the code (the function runExperiment) which turns the pumps on every 12*60=720 cycles (since each cycle is nominally 60 seconds).
You could to this in a similar way to the function already there to code the terminal which looks like this:

if(sysData[M][‘Experiment’][‘cycles’]%10==9): #Dont want terminal getting unruly, so clear it each 10 rotations.
clearTerminal(M)

In your case you would want it to happen every 720 cycles (i.e. set the top line to have %720=1 or something) and then when that condition is true, set the pump rates to whatever you want and switch them on, and if the condition is false (i.e. add an else statement below it) turn the pumps off.

[harrison]

Hello,

When you click “start” it will probably automatically set the pump rate back to zero, and it won’t necessarily Switch it on.

If you want the pump to run MANUALLY then you need to set the rate to something non zero (like 1) and then click “Switch” on that pump to turn it on.

If you want it to be turned on/off automatically then you need to set it into Turbidostat mode (i.e. “Start” the experiment then click “Regulate OD”) and then provided that the measured OD is less than the OD set-point it will intermittently turn on the pumps.

Does this make sense?

[harrison]

Great, glad to hear it is all sorted!
Thanks for the pics – indeed it is often hard to tell whether there is a short – even when you are looking down the microscope yourself, but it dose seem like a major possibility given how much solder is on there.

Harrison

[harrison]

Hi Jesse,
Seems like you have been through quite an ordeal, but made very good progress!

You mentioned the TCA9803 was one issue – did the soldering look bad on the original one? I am suspicious of the assembly, more than the chip internals, as with your spectrometer issues.
It would be worth telling Labmaker that you had these exact issues, which likely arise from poor assembly, since they are ultimately an issue on their end and need to be looked at more broadly to reduce issues like this (for you and others) in the future.

As to what to do next – it seems you have most/all of it working now. To be honest, I have never established some kind of “stress test” procedure for the devices. I have ~20 in my lab which I soldered entirely by hand and have never had any strange issues with the electronics on any of them. Once they are running fine, at least in my experience, they stay fine (ours have been used intensely for almost 2 years continuously).

One way you might test the whole assembled thing (short of doing an experiment) is
1) put a test-tube with ~20 ml of water and a stir bar into the reactor
2) Calibrate OD such that whatever you have in there reads at ~0.5.
3) Turn on all the FP measurements
4) “Start” the automated experimental mode
5) Set the OD target to 0.2 (or anything <0.5) and activate the OD regulation - but leave the silicone pump tubes disconnected from everything.

Doing the above would make the device heat/measure/stir continuously as in normal operation, and would also run the pumps at high-ish speed (since they aren't connected to the liquid every minute they would attempt to pump air, and continuously do this since the OD target is less than what it is measuring - hope this makes sense).

[harrison]

I think that is reasonable plan and aught to achieve what you are aiming for!

Keep in mind that both devices (Chi.Bio and the spectrometer) may be inaccurate at high ODs since it enters the “multiple scattering” regime. For example, this is why generally you need to dilute samples before putting them into the spectrometer when at high ODs…

[harrison]

Hello,
To change to LEDA or something else, you need to change the value I mentioned in sysData, which is defined at the top of the code.
You could then change one of those else if statements to catch whichever LED you choose (i.e. swap out LEDA for LEDD, assuming you want to use LEDD).
Then it should work as you hope, though it won’t be calibrated to align exactly with whatever benchtop spectrophotometer or plate reader you use. In practice spectrophotometers and plate readers can vary dramatically between manufacturers and devices, often by a factor of two or three!
So, if you want the Chi.Bio to match whatever other measurement device YOU have, then you would additionally need to do calibration by measuring a bunch of solutions on both the Chi.Bios and also whatever other device you want their measurement to replicate – as described in the paper Supplementary.

[harrison]

Hello,

To see how to do this check the function MeasureOD in app.py. In short what you need to do is change the value stored in sysData[M][‘OD’][‘device’] (by default this is ‘LASER650’ to something else (e.g. ‘LEDF’)) which will then mean the calibration and measurement OD functions will use this light source instead. There are different ways of calibrating this, depending on what level of precision you are hoping to achieve. Namely, you can calibrate just the zero-light level as usually done with the laser measurements. Or, you can go a step further and try to calibrate out inter-device variability, which you can see (some) code for in there already, and brief description in the Chi.Bio paper’s supplementary.

Harrison

[harrison]

Thanks for getting back to me with the detailed response. That all sounds good – I suppose it is a weird defect from the manufacturer of that chip.

I just checked on Digikey and I see what you mean – i’m quite surprised they are out of stock! Must be the continued global chip shortage…

Perhaps your best bet is to email AMS (manufacturer of AS7341) and tell them you have a chip that is faulty with an internal fault. Ask if they have ~5 of them sitting around they can send you as replacement. Often I find the manufacturers have small quantities on-hand to send people as samples…

I have gotten one off a breakout board and successfully resoldered it in the past, so you do have a possibility there. Soldering them back on to the Chi.Bio PCB is best done by applying solder then putting it on a hot plate.

Another idea, maybe you can contact Labmaker and see if they would send you an extra spectrometer board already assembled (though you said you already ordered another device so perhaps this issue is covered off…)

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