[harrison]

I do not entirely understand your statement. Wasn’t the stirrer already connected to the fan?
I think tape shouldn’t be able to fix this problem at least permanently – you’d need to add some m3 spacers (e.g. washers) onto each of the 4 columns below the heat plate to spread it out a little.

[harrison]

Did the above (looking in from the sides) make it clear what was going on? At the moment I believe that is the most likely solution…

[harrison]

Hello Patrick,

What stir bars are you using? If you have very large stir bars it might be enough to stall the fan.

Another thing – if you have already taken the sides off – put the vial + stir bar down to the bottom and look how much clearence there is between the top of the rotating part and the bottom of the resistors under the heat plate. I have seen a couple in the past where they touch and so fail, and this only happens when the stir bar is there pulling the fan up. If this is the case you could ship them back to labmaker and ask them to fix it. Even easier, though, would be to take off the fan and put some M3 washers in there between the vertical supports and the bottom of the heat plate PCB as this will space it out a little and prevent the crashing.

Harrison

[harrison]

Hello Jair,
Why exactly do you want this? If you are very concerned about stirring not being enough you could just reduce the pause between stirring stopping and the OD measurement.
The easiest (hacky) way to do what you want (if the above is not OK) would be to make the turning off/ON stirring parts of the code only happen 1 in each 20 cycles, and also set the OD reading to be such that it maintains the same value as the last 19 times and only updates once every 20th. But I really don’t understand what you gain by doing fewer OD readings. It will make the whole system much more susceptible to noise, and the OD regulation function will not work particularly well since it is only getting measurements a few times an hour, so likely it will massively over/undershoot the OD target. If you don’t want regular OD readings then just throw them out/average them out after the experiment

[harrison]

Hello Sofia

We have done both of these things in our lab at various points; using the white (6500K) LED at low intensity so support cyanobacteria growth, and also using CO2 to pump through the headspace. In the later we got a manual flow valve and connected it to a CO2 cylinder with pressure regulator and set it to some small flow rate (e.g. 0.1L per minute) which seemed to work OK. This was then just plugged into the top of each reactor.

[harrison]

Hello Robert
Are you using the pumps to pump air through the headspace? I suppose you could draw this from some high humidity source if needed. Not sure what else would be best.

[harrison]

Hello,
Yes it is, here is a paper in which set up Chi.Bio reactors with an Opentrons and various other pieces of kit:
https://www.nature.com/articles/s41467-022-31033-9

Also, all the software is already written in Python so if you are familiar with some SSH /webserver skills etc you can easily set it up to be controlled from your own external software package as the authors above have done. Or, you can easily enough implement different communications protocols (e.g. send HTTP requests to the Chi.Bio server that runs on the control computer to get it to do different things).

Harrison

[harrison]

Hello,
Let me correspond with the people who have done this recently and I will get back to you. You can email me if that is easier through the contact page on the website here.
Harrison

[harrison]

Hello Victor,

The original LZ7 LED is STILL used in the devices since the producer (Labmaker) bought a large stockpile of them when they saw it was going to be discontinued.
There are various alternate LEDs, such as the one you posted. However, at least in my opinion they are not as good as the original part we used. For example, in the case of the one you listed it has much wider PCLime and PCAmber filters which don’t give a nice “tight” excitation wavelength distribution, as is necessary to get good signal-to-noise for fluroescence measurements.

Depending oon your application you might be OK with this. In that case this WOULD be possible to swap into the device, though you need to check the pin-out on that LED is exactly same as the original LZ7 if it is to just be directly soldered onto the PCB.

[harrison]

Hi Ignacio,
As I mentioned in my email response, you need to use the CORRECT tubing. Which is 2.5mm ID 4.5mm OD as specfied on the Hardware page here: https://chi.bio/hardware/
Then, if you are still having problems, you could add tape to the pump head to make the seal tighter.
Ensure you have fully read the operation manual since it discusses each of these points (e.g. in the setup parts and also troubleshooting guide).
Harrison

[harrison]

Hi Silas,
Seems it would be if you had connected up the Atlas PH Sensor the ORP would be much the same, assumign you can get a probe that effectively fits into a (custom) lid of your design.

[harrison]

Hey Rob,
So far we have not implemented this broadly. Mostly people have either sampled the output waste or installed very thin PH probes into the lid. Or, some pH responsive dye that they put in their media and then measure colour change of.

For that paper – they are using phase angle of response to see fluorescence lifetime. I.e. it is not the physical angle of light incidence, but a proxy measurement for how long the emission delay is which one can measure with a high frequency modulation of the input LED. At present Chi.Bio would not be able to do this since the photodiode spectrometer wouldn’t allow fast (and synchronised) actuation and measurment (I think it at least needs to be in Khz range https://link.springer.com/chapter/10.1007/978-3-642-56853-4_13). So no, this is not possible. The LED might just be able to support that level of control given it can change PWM frequency, but even then it would be a square wave with some delay and messiness which would make it very tricky even if the right optical sensor was implemented.

[harrison]

AFter talking to our team they were surprised to hear you have GFP when using mScarlet only. What media and strain are you working with ? This might be down to autofluorescence of one or the other.

[harrison]

Hello,
Our team is usually using GFP at 450nm excite ~550 read, and then mScarlet at 595 excite and 670 read. Indeed the 620 read seems to bring a lot of GFP bleed-through, but this appears to be eliminated if you go even higher on the red edmission band.

[harrison]

Hello, I have gone through and added .step versions of each file to the Hardware page. Let me know how you get on with that, hopefully step is the most cross-platform-accessible format so most people will be able to use it.

[Author]

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