Okay, hello Foster. It's good to be back. My name is Joe, I'm a research for the University
of Glasgow, my second time at Foster, and my talk is about open research about something
called the open flexion microscope, and I've got it from two sort of directions. The research
using the open flexion microscope, we both develop it as a tool, try and improve it,
improve it, increase it's capabilities, but also look at the applications for it, not developing
it as a tool for tools sake, but an entire ecosystem of a journey of everything that is,
in some ways quite a simple device has gone further than I think anyone on the team ever
saw. So, this started with more technical issues. Well, that's a real shame. This started
a few years ago at the University of Cambridge with my boss Richard Beaumont, working
in an optics lab, and for the afternoon board question he was asking himself is, taking one
of the big metal expensive microscopes in the lab, how much of that can you replicate
at home using basic tools, a 3D printer, and off the shelf parts. And the answer
it turns out is quite a lot, otherwise I wouldn't be here. This was the early prototype.
You can see it's a couple of long way since then, but the idea of having three gears,
some plastic parts, and a Raspberry Pi camera, with a basic lens, it's really working
as a digital microscope. So, this was the first published piece of research about the open
flagship microscope, February 2016, so we're currently celebrating 10 years, and it was looking
out, again, basic 3D printers, basic off-the-shelf optical components, and what level of
performance you can get, combining those to make a translation stage, putting a slide on
there and using it as a microscope. It's all based around the idea of flex your hinges, hinges
that rather than parts, swining past it, which 3D printed parts are generally quite bad
out. Instead taking advantage of something that plastic is very good, which is deforming
reliably and repeatedly, the flex your hinges is what gives the stage its translation,
and the fact we are open is what gave open flexure its name 10 years ago. We take this
flex your hinge, put it in a few key places around the structure, and that lets us scan
around samples automatically. And the early paper was really focused on the mechanical
performance of it, the drift, the repeatability, the reliability and the precision. But
it showed that this is an approach that does work, you can use just the repeatable bending
of plastic to position something accurately enough that you can use it as a microscope.
And from there, the research into open flexure really started. So, we wanted to use the
Raspberry Pi camera for quite a few reasons, but it is, I think, fair to say, and I don't
think anyone here would disagree with me, not exactly what the Pi camera was designed
for. And so, the early question was, well, is this going to work? Can we calibrate the,
it's okay? Can we calibrate the collar to make it a true recreation of the sample when
we're not looking at something that's 2, 5, 10 meters away, we'll look at something that
at times is only a couple of microns away. Here you can see on the left of the before,
I don't know how well the projector is showing this, of applying green, blue and red sample.
This is after calibration. And also, how are we going to do this in a way that's not just
open but repeatable? And, done in a way where we can go through our history, and we learned
a lot of lessons from open software development. Our microscope is designed in open
SD card. It's a programming based CAD package. That means that we get the same version
control as any software development team. It means that when we change the position of
something or the height, we can see that in the history as physical code that's changed
to move the physical parts. That also means that we can do what we called hardops, so using
the GitLab CI to automate a lot of hardware steps. So, mad as this kind of sounds as
a phrase, we link to our hardware. We automatically rebuild it every time something's
pushed or merged. As part of that pipeline as well, we automatically redo all of the vendors
that are in our instructions. It sounds like quite a cute line to say we've spent more
time on our documentation than we have on the physical design, but I can show you the
time sheets, it is 100% true. A big part of that is making sure that we're reaching as many
people as possible who aren't confident engineers or builders. And one thing that we've
got is feedback quite often is the photos in your instructions don't match the parts that
I've got, which was often, you know, we changed the size of a gear or the angle of a hole,
something like that. It's one of the fundamental we didn't matter to the build, but still
people who weren't confident, would he be able, I'll just say quite often. Instead, when
our automatic we rebuild all of our vendors that are in the instructions every time there's
a change, and as part of that, we also have the release on the outside and the GitHash to build
those parts on the inside. That means that we can make sure that everyone's on the same page
with the hardware, it means that if I'm working with a collaborator who swears 100% absolutely
that they did print the right part, I get to go in and check. So it's a popular feature for
me, but some of the collaborators may be not so much. We also worked at how we can compensate
for some of the inherent limits of this approach to building a microscope. The hardware,
I'm sorry to say, is not as precise as a half million pound-side scanner straight out
of the box. Some people come up to our store and tell us that as if it's some sort of
gotcha. But we listen quite smart with this digital microscope, and that's, we put a sense
of in there. So that we can monitor how successful it is moving and working. We're using
the pie cover. So if the things like this, we can, when looking at blood smears, check our
focus as we're going. This is looking at a blood scan on the upper plate of microscope,
when you're 10 microns out of position, 5, 3, 2, 1, and in focus. We know what this looks
like. We can self-calibrate our movements now scanning as we're going rather try to solve
everything at hardware. Working on the software, we align it with the web of things inside
every microscope is a Raspberry Pi that spins up a web server and controlling the hardware
as a simple HTTP request. That means that a lot of people have got in touch saying that
they only wanted part of the microscope and wanted to bring some of them in hardware and
everything into faces seamlessly. It also meant that someone got in touch saying that they
had done open-flight surveillance control for example weaving the microscope in a few
in the cupboard, or an incubator, and blockly. So being in programming to people who aren't
comfortable with programming. We also have some more dead links and two sort of spin-out projects
to the delta stage and the block stage. Same approach in terms of how far can you take
flexure-based 3D printing. All of the same approach of how can we make this as open as
accessible as possible. We published our version 6 of the microscope paper a few years ago
now where we're talking about all the capabilities things like for the SNS imaging, reflection,
transmission, all the different imagery modes and things that we've developed over the previous
few years. This is rough. Well, it means I won't run over time. And then we also shared
a lot of our experiences because we were co-developing this with a team in Tanzania and we do
mean co-developing. And that is in some ways very, very challenging. And some of the lessons
learned about how to co-develop something with partners in Tanzania when, for example, it's March
2020 and your fight has just been cancelled. We were over there just as Heathrow Airport shut
down during COVID so that was about the most stressful work travel I've ever done. And that
we've come to this a 3D printed automated microscope with customizable optics, with different
imaging modes, running a fast API server. And the first rule of talks in engineering is never
given live demo. But considering how well my slides have gone, maybe this is for the best.
So this is a live stream from the microscope. You can either trust me that it's live or I can do this.
And if anyone thinks that I've time to that perfectly, you're more paranoid than me.
But this is the research that's going on to the microscope. Now at the University of Glasgow,
and a few other research places, things like the auto focus that I've just done, clicking around
the sample, capturing images, calibrating everything. So if, for example, you just flown with this
microscope through Edinburgh Airport and security weren't too sure about it. And they decided to test it
by giving it a little shake. We could also calibrate for that. That also means that if you're not confident
in your printer or in the parts that you've got, this self-calibration runs automatically,
giving you a report on whether or not the stage is moving as expected, whether or not the camera
can calibrate properly. One of the big projects that we want to work towards the next couple of
years is a fun calibration report. So when we launch version 7 of the microscope, people could
run this calibration, send us the report and we can start mapping what the limits are. Is it
in certain areas where people use a different supplier or our instructions are clear enough to
people with English as a second language, things like that, mapping up what are the actual challenges
around reproducing hardware around the world? Now it's hope that that calibration works.
There's stuff. From here we can also do automated scanning and this has been a big focus of our
work, the last few last couple of years, not just scanning a single field of view, but doing an
automated scan where we can capture a VFocus and move around building up huge stitched images,
like this, for you automatically getting the kind of detail you need to see inside a cell,
it looks even better not on a projector. Variable for hobbyist, valuable for engineers,
potentially invaluable for people like pathologists who are overworked and don't have the
funding to hire the number of people they need to be scanning samples and spending time with patients.
And that kind of would be it, as I'm having the five minute sign, where you've got me,
but there's also all the people we've got in touch with broken lengths as well. Not one
after we launch this, something started happening because we did something that seems insane to
anyone, maybe not in this room, which is that we made this open source and as accessible as we
could as well documented as we could and it wasn't long until a research group at a different
university contacted us saying, hey, we've found your design, we've modified it to do super
resolution microscopy. Cool. Or a team out in Japan got in touch saying, hi, we've modified your
design for structure the illumination. So physically moving or grading around a filter out of
adding out of focus light to get resolution higher than you would be able to on this otherwise.
We've done that, we've taken all the data, we've published the paper and we thought we'd get in touch,
we hope you don't mind. We didn't. For how they were able to modify the hardware so easily,
I should put you towards Julian's talk this afternoon at 140. People also got in touch sending us pictures
of, come by the store later, I'll show you the actual pictures. People got in touch showing the
workshops, they've run with the education workshops, engineering workshops, also commerce workshops
setting up the idea that people can sell this and turn a profit and support the community that needs
more hardware, more technicians, more people using microscopes. And then people also started getting
in touch saying that they'd used our microscope, not because they were interested in a 3D printed
microscope, but because they needed a microscope and we were the best option available to them for
one reason or another. And that became a bit of a transform for this where we've started to feel
like we were just part of the scientific landscape, rather than being the novelty for someone who
wanted to try out 3D printing, we were part of the microscopy world. People also got in touch
a lot about healthcare applications, so a team in the Philippines got in touch saying that we've
shown that your device has the ability to look at samples for tuberculosis, heart disease,
and multiple other conditions, and it works. Dr Daniel Rosen, a professor of pathology over
in the United States, is one of the big people who's been driving this project forwards,
no engineering background at all, but I think at this point now is 6 3D printers in his shed.
And he's been telling us, you know, you guys don't know what you made, this wasn't just a microscope,
this is a slide scanner, digital slide scanner, which is prohibitively expensive for
the majority of the world. He worked with us, he's published papers using our microscope to image
cancer in the esophagus, and was also the driving force between a recent trip we had to
so power. Hospital DMR in so power is the main cancer center for the country, and as part of that
work, they buy trucks, strip out the back of them, and turn them into a lab, and that lab,
goes and parks up wherever it's needed across the country, and where I say goes wherever it's needed,
there is an incredible picture there, which has not worked with them floating one of these on a
barge down the Amazon. So if anyone ever asks this open flex, if available on Amazon,
we also use this platform for open pathology education, because the digital images that come
off this microscope can be used for education, and it means that some of our collaborators in
underserved regions can now run online lectures on a digital scan of the samples from cases
that they see every day in their practice. The alternative is everybody gets trained on the same
digital scans from areas of Europe and North America. It doesn't reflect the sample,
doesn't reflect the conditions, doesn't reflect the sample preparation, that the majority of
doctors around the world are looking into. We set up a forum so that people can start sharing their
questions and ideas and work with us, and also set up a YouTube search alert, and these are people
that are off and outside of academia, who there's no conventional academic way to ever reach out
to people who had a 3D printer, were happy ordering parts online, and then you're doing things
like machine learning on the pie to label various features of their samples from the forum as well,
literally someone got in touch, I don't know his real name, saying that he was going to adapt
this to do a top atomic force microscopy, to give you an order of scale that's going from looking
at individual cells, to looking at individual atoms on this thing, and we thought, it's a
lot of way idea, and then the schematic started coming out of his apartment in New York,
some of these schematics had to be read on, because his children found them and thought that they'd
help by colouring them in, and he now has a prototype, and just a reminder of his images continue
to fail to load, that's where all of this started, and now we're here and with dozens of other projects
I could tell you about, this is our world map of every country where someone's got an
in touch with us saying we've built or used your microscope, and as much as I wish that this was
me flying to 70 different countries with this in my hand luggage, that's not the case that's
people finding this organically and getting in touch, the map tells half the story, but it's the
people involved, the fact that if you put this out there people will find it and use it for things
that you never thought were possible, or maybe even a good idea, and that's as far as we thought
it would go with that world map with all the different countries coming in and hopefully every
few months will be able to add one or two more, and then on LinkedIn we saw this a couple of months ago
a group looking at immune cells in microgravity needed a microscope that they could adapt,
it had to be lightweight, and it had to be something that was open source so that they could
interface with other components, and so our world map, as of March 2027, is going to be a bit
obsolete, and we're going to be doing a world gift instead. I'll finish with the conclusions from
that first 2016 paper, written before I was on the project, and highlight this microscope is
a useful tool on its own right, and there is much potential we plan to further investigate in the
future, so in ten years essentially nothing has changed. I'd like to thank you all for listening,
I know that I've got a swap that many of you wish that you didn't have to get up for,
we have a stool just along here, and two more talks from members of the team on the educational
applications and on the hardware journey itself. I'm very excited to take any questions, and you can
find it out there until the end of the day. Thank you.
Okay, well, we'll do, okay, thank you.
In Antarctica, is using my requires strong words? The question was, do we know who was
using the microscope in Antarctica? So the users per pixels in Antarctica is pretty good. It was
a biologist a few years ago who wanted to take samples of the ice, triage them out in the field,
so to speak, and then take the samples that looked interesting back to her lab. She's not on the project
any more, but we're always going to be grateful for the work that she did. Is that else?
Yeah, of these companies that sell the microscope. Yes.
Now, Lord, you're skimmed, it's down with everything, and then you sell it to yourselves.
Do you have any arrangements with them in financial arrangements?
We have a, yes, so we do have, as you say, I think it's 12 vendors around the world at this point,
who have got in touch saying that they'd be interested in selling kits for the microscope.
Our license is very clear that we can't stop them, but we also don't want to.
And we have regular meetings with them, we have a memorandum of understanding. Some of them voluntarily
gives some of the profits back to the charity that supports disk growing network, others instead
contributes to the code base, things like that. And then on our website where there's a list of vendors,
we try to give it an idea of what contributions each of them voluntarily make.
But to be honest, the contribution of them selling it is already enough of a contribution,
because I don't like counting out screws and small bags. So, thanks, guys.
Please.
Is there any concession with the other, if you like, of course, a key platform?
Are there any concession for the...
Okay, so a question, first thing in the morning about our API have on and working with other
open microscopy.
I'm not aware of anything with four men go, but what you're doing?
Okay.
It means a bit, but for example, you see two of anyone's familiar with Benedict Deedrick's project.
It's a series of modular cubes that all slot together so you can build an optical path.
As long as you want, we don't quite have the space for that in here.
So a few years ago, we worked with Ben A to print a little adapter plate,
by essentially he bought the optics and we bought the stage, and they interface perfectly.
Anything else?
I'm really inspired to use a new process to another organization with a particular adapter
as create a model for you. Is there a code review for the hardware you built it, how does that work?
Oh, yes, so this code review for the hardware is much as this for the software.
People have folks this and then modify it in different ways, quite often it's things like they only
wanted, perhaps the Z control rather than the XYZ control. Sometimes they'll live as folks,
but other people do get in touch saying that I think this is something that everyone would
be interested in. Our documentation also has a list of customizations and other versions,
which is where some of those live. So our microscope's unusual in that we have the camera in the
base and the illumination at the top. There's a customization for this, which isn't as vigorously
tested where that's inverted, but yeah, the code review for the hardware is a huge part of what we do.
How was the time?
Yeah, thank you so much, thank you so much.