DR4000U Repair and Filter Notes

I have a DR4000U photospectrometer that I bought as junk on eBay. After installing a new UV lamp the instrument powered up and passed power on self tests. I could take measurements and at a first glance things seem to be fine. However… on closer inspection almost all samples showed negative absorbance. The only way I could see this happening was if my samples were strongly fluorescent or they were somehow acting as an optical element reflecting light into the reference photodiode or perhaps focusing more light on the sample photodiode. But this proved not to be the case…

Using the instrument noise checks I also noticed that blocking the light path completely also resulted in negative absorbance. This makes no sense. Eventually using the noise check to look at the photodiode current I figured out something wrong with the instrument. The reference photodiode seemed to increase when I shined a light on the sample photodiode.

After comparing the wiring to another DR4000 I realized that someone had swapped the sample and reference photodiode inputs. This is relatively easy to do as they are both just connected using identical coax connectors. But what’s more interesting is that this /kind of/ works. That is all the power on self tests, which include scanning the grating and wavelength calibration (against the filter wheel references) worked.

So, this seemed like an easy fix. But when I switched the cables round the unit failed wavelength calibration. I then switched out the filter wheel with a working (visible only) DR4000 and the unit worked correctly. So, this instrument had a dead filter wheel, but somehow switching the reference and sample photodiodes tricked it into thinking more light was being detected than actually was, and the instrument passed calibration.

I will probably run this unit with the new filter wheel. But I’d also like to be able to replace the filters in the other unit. Below I’ve taken spectra of the good and bad filters. It might be possible to figure out what filters I need to get to replace these. Hopefully I can also dig up some further documentation somewhere.

Filters

I’ve numbered filters as shown in the image below (hopefully you can just about make out the scratches). This image is from a bad filter wheel. Physically the old but working filter wheel I have looks about as bad as this however, so I’m not sure you can tell an “ok” filter wheel from a bad one visually. In all likelihood the filters I have are all in poor condition however.

“Bad” spectra were taken from the instrument mentioned above. It failed wavelength calibration with “24: Monochromator error”. As mentioned, when the filter wheel was swapped with another unit the previously broken instrument started working. Each filter was illuminated with a Xenon light source and jammed up against a spectrometer head. Possibly not very accurate but may give some indication as to the nature of these filters.

The images below were taken from the “bad” filter set. I tried sticking them in the spectrophotometer and measuring their absorbance. The filters were however in the wrong orientation. Could possibly be instructive however:

Newport 841-P-USB (Black case) Notes

I picked up an old USB optical power meter on eBay. This meter is on longer supported by Newport, and they don’t list it on their main site. If you go to their download site (https://download.newport.com) you can find software for the 841-P-USB, but as far as I can tell this is for a newer version of the instrument. The device does not appear to work with PMManager or any of the other software Newport currently support.

It looks like there were two versions of the 841-P-USB, and earlier “black case” version and a newer silver case version. The silver case version seems to have an expanded command set, and possibly runs at a faster baud rate.

However, you can talk to the 841-P-USB over serial and get data out of it. You should use 57600 baud (8N1). The 841-P-USB manual (for the silver version, which you can find on the site above) lists several commands. I used the following to take measurements:

*SOUZero offset
*CVUTake single measurement
*CAUPrint continuous measurements
*CSUStop continuous measurements
*F01Show device and sensor information
*PWC00000Set the wavelength used for connection (e.g. *PWC00532)

If I do find any software that works with this instrument, or further information about the device. I’ll update this blog post.

Inside the Lucira Check It COVID-19 Test

This post was previously published on the substack.

The Lucira COVID-19 test is an “at-home” LAMP qPCR-like test. Essentially you receive disposable molecular test device, with embedded reagents for $55 which you use once and then throw away.

I was curious to better understand the instrument and went hunting for teardown pictures and patents. Luckily Brad Ackerman on pulled one apart and posted pictures on twitter. Some of these are included here with permission from Brad. The teardown pictures also closely match one of Lucira’s patents which gives us another source of information. The patent has some wonderful figures, and gives us a really nice exploded view of the device:

This really gives us a great overview of the instrument. We can see a single main PCB with contains LEDs, a photosensor, heating element, temperature sensor and microcontroller. The heating element is a simple PCB trace used for resistive heating. This is required get the reaction to ~60C as required for LAMP. Critically, for LAMP we don’t need do thermo-cycle, so cooling is not required. 

The photosensor sits in the center of the heating element, surrounded by LEDs. On top of this there’s a reasonably complex optical system:

The sample will flow down from the prep tube and be exposed to a reagents ending up in a number of fluidic chambers. This is kind of neat, because as we can see in the image above each LED is paired with a chamber. The light from the LED is reflected through the chamber and down on to a single photosensor.

This allows you to multiplex to some degree, using a single sensor and multiple LEDs which you can switch on/off. Naively you might think that for COVID-19 you only need a single measurement. But the FDA authorization makes it clear that the device also has a “Positive Internal Control (PIC) and Lysis Internal Control (LIC)” which must also show the expected results.

Looking at Brad’s teardown images, we can see that Lucira have only placed 4 of the possible 8 LEDs in the COVID-19 instrument. So Lucira could potentially expand the capability of the device to other targets/variants:

I wasn’t able to identify the photosensor used here, but I suspect it doesn’t cost more than $1, similarly the LEDs likely cost almost nothing. The microcontroller is an STM32F030C6, a simple 32bit ARM microcontroller with 32K of flash, 4K of RAM. This also usually costs ~$1. Overall I suspect the BOM cost is somewhere in the region of $5. The photosensor could potentially be the most expensive part if this turns out to be a high sensitivity photodiode…

The optical system appears to be all plastic, here you can see the light pipes. They show up as different colors, it’s possible there are embedded filters. You can also see the heat conductive paste that is used to couple the heating element to the rest of the unit:

The result of all this is a platform, where much like qPCR, you can monitor the amplification process in order to determine the presence/absence of your target. The patent shows some example experimental data:

While I suspect the electronics doesn’t cost much, I’m still impressed they can sell this for $55, as it’s a reasonably complex optical/reagent system. I’d be curious to know what their margins are. Overall I find the approach pretty neat. No doubt BARDA (who gave them $21.9M in 2018) must consider this a prescient funding decision.

Lucira IPO’d in February, but it seems that their share price has been rather unstable. It will be interesting to see what happens with Lucira and if they and gain adoption outside of COVID19 diagnostics.

Roswell Revisited

This post previously appeared on the substack.

I’ve previously talked about Roswell. But they’ve recently been making a bit more noise, and I thought It would be interesting to review my previous post in light of this new information.

Roswell was founded in 2014, back in 2018 they were reported to have raised $6M. Cruchbase now lists them as having raised $37M though it’s not clear how recent this figure is. A recent Genomeweb article says they now have 50 employees.

Roswell’s patents show a basic configuration where a strand of dsDNA is suspended between two electrodes as a kind of scaffold. A polymerase is then attached to this scaffold. The polymerase performs synthesis of a template strand and conformational (and other changes) are detected:

Detection is likely through tunneling (and potentially other) currents between the electrodes. Conformational changes in the polymerase and/or incorporated nucleotides would result in current changes that could be detect to sequence the strand under synthesis.

The patent I previously looked at showed data from homopolymers, with current defections on the order of 60pA.

So what’s new? Well, if the animations on their website are anything to go by, the basic mechanism is still broadly as described above:

Roswell’s whitepapers also help clarify this process, where an electric field is used to attract the bridge molecule (dsDNA). The approach seems pretty neat, as you can turn on the field, attract and attach the dsDNA and then immediately turn off the field. This means that you should be able to attach a single bridge molecule to each sensor. Without something like this, you would be Poisson limited, with many sensors having no, or multiple bridges.

The Genomeweb article suggests they’re shifting away from DNA sequencing and “targeting diagnostics, especially for infectious diseases, or drug discovery as its first applications”. This is perhaps because their sequencing accuracy isn’t quite competitive yet:

“”Discrimination of the four bases can approach over 90 percent, and in complex templates, 70 percent,” Mola said.”

It’s difficult to unpack this statement without knowing exactly what experiments were performed and how the data was processed. But to me it suggests they’re not quite sequencing yet, but rather looking at ensemble properties of synthetic templates.

The white paper also tends to focus on applications other than DNA sequencing. For example hybridization based assays:

I personally find these other applications less compelling than sequencing. The advantage over other approaches, including other single molecule approaches, is unclear to me. But I do find the fact that the approach works at all, kind of exciting.

The other nice feature of the Roswell approach is that they can potentially pack features much closer than you can on a protein nanopore chip. The density they show, of 2500 sensors per mm² seems pretty good.

Roswell Gen3 chip: 180nm process, 4x6mm die, 1KSPS (per sensor)

This is an advantage because it keeps the chips relatively small. Roswell’s Gen3 chips are 4x6mm. When I last looked at image sensor pricing, it seems like chips of this size would generally retail for about $10.

That’s pretty cheap, but still an expensive COGS for a consumable, which given the approach I suspect is not washable/reusable. This potentially makes the approach unsuitable for low-cost diagnostic applications.

However, that their approach works at all is neat, and I’ll be watching Roswell’s progress with interest.

Disclaimer: As always, you should be aware that I have equity in sequencing companies (based on prior employment) and am current working on a novel sequencing approach.