V7.0.0-beta1 Build Report


I recently decided to try and build an Open Flexure microscope. My current end goal is to build a single beam confocal laser scanning microscope, very similar to Breaking Taps build. As I’ve never built anything like it before, I decided to start simple and build the basic microscope.

I built the High-resolution microscope v7.0.0-beta1.


To print the parts, I used a Bambu Labs X1C. I printed all of the parts at 0.28mm Extra Draft, 15% fill grid, and Slice gap closing radius at 0.001. The total print time was about 10 hours and used about 350 grams of filament. Removing the brim around the main body was trivial and did not require a knife.


I ordered 3 50mm acromatic doublet lenses from Surplus Shed for $7.50 each, plus $6 shipping. It shipped out the next day (Friday) and arrived Monday (3 days later).

I bought the 30mmx34mmx2mm O-Rings on Amazon (https://www.amazon.com/gp/product/B07ZDM58S8/ref=ppx_yo_dt_b_asin_title_o00_s00?ie=UTF8&psc=1)

I bought an AmScope 40x Achromatic objective for the microscope.

I am using a Raspberry Pi 3 with an Arduino Mega and 3 28BYJ-48 stepper motors plugged into ULN2003 driver boards. I am using a standard Raspberry Pi Camera v2.

I bought these Optical Convex Condenser lenses from Amazon (https://www.amazon.com/dp/B0BR5PYPQB?psc=1&ref=ppx_yo2ov_dt_b_product_details). It just barely fits and will fall out if you bang the table so it seems 12.5mm may be too small and 13-13.5 may give a better fit.

For the LED, I printed the LED workaround and I am using a standard 5mm warm white 20mA/3-3.2V LED with a 150 ohm resistor.

I bought some 0.5mm white styrene sheets but they appear to be too thick because they block a lot of the LED’s light. Removing the sheet from under the LED did not seem to have too negative of an effect on the image.

I used 20mm instead of 25mm screws for the gears. I was not able to find any 25mm screws locally so I just ran with 20mm. They appear to work just find, but result in a slightly diminished scan range.

The nuts I own appear to be flat on both side and I could not tell one side being curved. I don’t know if this made any difference. I just stuck the two nuts together and everything worked in the end so.


Putting together the microscope was pretty straight forward and for the most part it was easy to follow along.

I did need to reference the ‘livestream’ video once or twice to fully grasp what needed to be done. The main place I referenced was

## Step 5: Attaching the viton bands and foot

It is not very clear from the images what orientation the foot should be in and that the O Ring should go in the groove like.

The Arduino workaround does not specify which pins are what, only that it uses pins 2-13. I would have liked to know that X is pin 2-5, Y 6-9, etc. I had to guess and check. I am powering the motors using 5V out from the Arduino with success.

The Objective appears difficult to screw in perfectly to the optics holder so that it’s not slightly off angle. This is most likely just a flaw with 3D printing threads itself.

With mounting the optics to the body, my screw is quickly being stripped and I will probably have to replace it if I unscrew it and remount it too many more times. I think being at an angle makes it difficult. I am not sure if using a stronger metal for that screw would help much.

The long screw in the illumination appears to serve no purpose with this build. I have no issue with the illumination falling.

The sample clips appear to be a poor design for how I use them. I rotate them get a better clamp down on the slide and doing so quickly loosens the bolt. I don’t have any ideas or suggestions about how this could be better at this time.


I installed the Raspbian OpenFlexure full desktop on a 256GB SD Card. I have only interacted with the microscope over the web browser so it appears I should have went with the Lite version instead.

The software is really great compared to a lot of other scientific software, but I think there is still a lot of issues and improvements that could be made. I am not sure how much of what I’m about to say has been changed or not.

The biggest issue I had was that it is not well documented what to expect from 40x images and that the focus distance to the slide is very close. It’s so close that I realized you needed to flip the slide upside down to achieve proper focus. This is not a software issue, just maybe a section on the User Your Microscope page that quickly talks about what to expect from 10x, 40x, and 100x would be greatly appreciated. Something like “Here is a sample 40x image you should expect to see. You should expect your objective to be less than 1mm from the slide. Here is a sample 10x image you should expect to see. You should expect your objective to be Xmm from the slide.”


I did not read the readthedocsio page about using the website so this is my process and thoughts about using the website going in blind. I think the basic layout of the website is good.

It’s super annoying there is no “stop” button and no current position indicator. Use case: I’m at -3000 Z. I enter 3000 Z. I want to stop when the slide is in focus rather than scrolling on the mouse 1000 times. Not only is there no way to stop, once it’s finished I have to guess the position the focus or point of interest position was at.

The autofocus seems to work terribly for me. I feel like Fast misses more than it hits.

Manual Focus:

Manual Focus

Fast Focus:

Fast Focus

I’ve also had a lot of issues with medium and fine. Medium doesn’t seem too bad but it appears there is a limited range. So if it’s, say 1000 Z, out of focus, medium will not find focus.

For some reason, my slides are “slanted”. If you move in the X direction, it’s almost always in focus but as you move up or down in the Y, it gets more out of focus from the starting focus point. I have no idea why, other than the objective is not parallel with the body but I have no idea how to fix that.

Stack and Scan is very cool. I have had issues with some kind of timeout though. I should have written down the logs. I also hate that clicking on “Storage” does not automatically refresh captures. It has gotten me more than once scanning the same slide in the same starting position where it wasn’t updated and I tried to download an older slide.

Here is a stitched together slide:

Zea Seed L.S.
x step-size 1200
y step-size 1200
x steps 16
y steps 16
z steps 1
Autofocus Fast
Scan Style Snake
Naming Style Coordinates

I would really love to see the ability to stitch together the slides on the site itself.

I have quite a few other notes but I think this post is getting a little long and not really sure how useful they will be.

Overall, I am pretty impressed with things and look forward to seeing how things continue to develop. I am currently printing the Delta platform and look forward to getting that a try as well.


Additional single image scans at 40x:


Hi Whiskey,

Welcome to the project and thanks for such a comprehensive write up! All that information is really useful, and I’m glad you worked through the issues

For now, looking at your software feedback, I’m happy to say that a future version that we’re developing addresses most of them. You’ll be able to “stop” a move or scan, the autofocus will self-test whether it succeeded, the gallery will self-update live, and you’ll get a live preview of the stitch in the software. More than happy to share a copy of this software if you want to test it out, but it is in pre-alpha so please expect a few bugs

I’ll take a look at your hardware issues later on - we’d expect you to lose focus as you move in x-y because of the design of the stage, but it’s strange that you’re seeing it more in one axis than the other. The main way to mitigate this is to make sure that you’re starting your scan from the centre of the stage

For the build, we can look into adding some more renders, and would you find a better edited video helpful? And maybe another document / video with using it for the first time?

Seems like I’ve matched your essay with an essay, thanks again for sharing how it all went for you

I will definitely continue to test. The last few days the objective was more towards the edge so I went ahead and did a scan with the objective more centered and maybe it was the sample, maybe not, but it does seem to have better focus throughout with autofocus off. I am currently scanning the other one again right now using spiral with autofocus off to see how the results look and if there is a line of in focus and out of focus or not.

Tilia Stem CS
OpenFlexure Microscope
High-resolution microscope v7.0.0-beta1
Stack and Scan
x step-size 1100
y step-size 1100
x steps 12
y steps 12
z steps 1
Autofocus Off
Scan Style Spiral
Naming Style Coordinates
Zoom 40x

Full Resolution

Here is the same Zea Seed slide from the original post but with Spiral, no auto focus, starting scan with objective in the middle of the platform (sorry for poor stitch quality):


Really nice build. You are the second one that mentioned using the X1C. How do you like it?
The out of focus area was mentioned before on another thread. In my case was using semiplan instead of plan objectives. Using a 40x plan there is essentially perfect focus. What are your objective specs?
Those motor driver boards on top of the raspberry make me nervous. :slight_smile: :confused: someone recently posted a mod to fit the drivers and pi.

I guess the listing for my AmScope A40X does not say if it’s plan or semi-plan


I did not leave the motor controllers on the raspberry pi for long haha just for when I took the photo.

I love the X1C. I’ve been using 3D printers for a long time and this printer is the first time I’ve truly felt like the printer “just works”. I click print and basically a perfect print comes out almost every single time. The bed is always level and it’s crazy fast. My dad replaced 3 CR-10s with 1 X1C and it’s faster than all 3 at once and the prints turn out better. They’re expensive and not open source, which is something that I really don’t like but I can’t argue with the results.

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That is the same one I’ve got the first time. it Is semiplan and in part (if not all) the reason you have focusing problems.
This conversation thread I had with @Yashka was very informative for me. Explains plan vs semiplan.


Follow up: I printed the objective holder at 0.12mm height and the objective fits way better. I would highly recommend printing that part at a much smaller layer height if you’re printing the majority of stuff at 0.28 draft.


On my Prusa, I printed the optics module with 0.2mm layers except for the the objective thread section at the top, which I configured to print with 0.1mm layers. Since the thread is 36 tpi, or ~0.706mm pitch, that’s almost optimal.

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