[Nition]

I always love the moment in blog posts like this, where the writer with their esoteric knowledge of the project will say something like "I almost considered reflaboring the exahenge, but of course it would be a ridiculous prospect for a project of this type". And then always, inevitably, there is the followup edit; "I reflabored the exahenge."

Too rarely in life are things made better than practical consideration would dictate, just because of dedication to the craft.

[dekhn]

History is made by people who reflabor the exahenge.

I build microscopes instead of telescopes (as a hobby). I can't tell you how many times I've taken a mostly working system and stripped it down to make some important change that affects most of the design to get only a tiny incremental improvement. Sometimes that improvement makes all the difference (for example, being smart when 3d printing a piece that carries something heavy so it doesn't deflect) and sometimes it's just an itch I need to scratch. Eventually, I learned to make two: a microscope that gets built and used, and then a microscope that is a prototype. Then I'm not tempted to take the daily driver and pull the engine.

[cadr]

Ooh! Tell us about microscope making as a hobby!

[dekhn]

Uh, OK. So a few decades ago a scientist I respect built his own scientific tool from parts (https://www.nature.com/articles/35073680) and I was really blown away by that idea, especially because most scientific tools are very expensive and have lots of proprietary components. I asked around at the time (~2001) and there wasn't a lot of knowledge on how to control stepper motors, assemble rigid frames, etc.

Although my day job is running compute infra, I have a background in biophysics and I figured I could probably do something similar to Joe Derisi, but lacked the knowledge, time, and money to do this either in the lab, or at home. So the project was mostly on the backburner. I got lucky and joined a team at Google a decade ago that did Maker stuff. At some point we set up a CNC machine to automate some wood cutting projects and I realized that the machine could be adapted to be a microscope that can scan large areas (much larger than the field of view of the objective). I took a Shapeoko and replaced the cutting tool with a microscope head (using cheap objectives, cheap lens tube, and cheap camera) and demonstrated it and got some good images and lots of technical feedback.

As I now had more time, money, and knowledge (thanks, Google!) I thought about what I could do to make scientific grade microscopes using 3d printer parts, 3d printing and inexpensive components. There are a lot of challenges, and so I've spent the past decade slowly designing and building my scope, and using it to do "interesting" things.

At the current point, what I have is: an aluminum frame structure using inexpensive extrusion, some 3d printed junction pieces, some JLCPCB-machined aluminum parts for the 2D XY stage, inexpensive off-the-shelf lenses and industrial vision camera, along with a few more adapter pieces, and an LED illuminator. It's about $1000 material, plus far more time in terms of assembly and learning process.

What I can do: the scope easily handles scanning large fields of view (50mm x 50mm) at 10X magnification and assembles the scans into coherent fullsize images (often 100,000x100,000 pixels). It can also integrate a computer vision model trained to identify animacules (specifically tardigrades) and center the sample, allowing for tracking as the tardigrade moves about in a large petri dish. This is of interest to tardigrade scientists who want to build models of tardigrade behavior and turn them into model organisms.

Right now I'm working on a sub-sub-sub-project which is to replace the LED illuminator with a new design that is capable of extremely bright pulses for extremely short durations, which allows me to acquire scans much faster. I am revelling in low-level electronic design and learning the tricks of trade, much of which is "5 minutes of soldering can save $10,000".

I had hoped to make this project into my fulltime job, but the reality is that there is not much demand for stuff like this, and if it does become your job, you typically focus on getting your leadership to give you money to buy an already existing scope designed by experts and using that to make important discoveries (I work in pharma, which does not care about tardigrades).

Eventually- I hope- I will retire and move on to the more challenging nanoscale projects- it turns out that while you can build microscopes that are accurate to microns with off-the-shelf hardware is fairly straightforward, getting to nanoscale involves understanding a lot of what was learned between the 1950s and now about ultra-high-precision, which is much more subtle and expensive.

Here's a sample video of tardigrade tracking- you can see the scope moving the stage to keep the "snout" centered. https://www.youtube.com/watch?v=LYaMFDjC1DQ And another, this is an empty tardigrade shell filled with eggs that are about to hatch, https://www.youtube.com/watch?v=snUQTOCHito with the first baby exiting the old shell at around 10 minutes.

[cadr]

Having it automatically follow tardigrades is so cool! It sounds like great fun. Did you make the ML model for tracking them?

I've wanted to make this the Openflexure Microscope (https://openflexure.org/projects/microscope/) but it is behind the backlog of all sorts of other things.

[dekhn]

Yes, I took an existing vision model that could run at realtime on my laptop, and fine-tuned it with a few hundred manually labelled images of tardigrades.

I don't like the openflexure design at all. I mean... obviously it works for a lot of people, but I just don't want a flexure based stage. I like real 2-axis stages based on rolling bearings, basically cloning the X and Y parts of this: https://www.asiimaging.com/products/stages/xy-inverted-stage...

UC2 is another cool project: https://openuc2.com/ but I found their approach constraining.

Frankly I think you could just buy an inexpensive 3D printer that had an open firmware, and replace the extruder with an objective, a tube, and a camera, and you'd have something up and running cheaper for less time.

[taneq]

Well yes, but are you wiggling the giblet or are you flensing the grobbulus? Because the latter requires specialised equipment and a flensing trampoline, whereas the former requires a 1mm Allen key and possibly a hard whack on a nearby surface while nobody’s looking.

[dekhn]

Flensing trampolines are out of my budget, so it's just giblet wiggling for me.

[Nition]

I've seen a few people flense without an f-tramp using a retro-stabilising grob clamp instead, if you've got one.

[chantepierre]

Your comment brings me back to my first mirror making adventure, I was absolutely overwhelmed by the jargon and acronyms used by the mirror making community... a few years later I internalized it and use it as if it was common knowledge. I should put little explanations or details in my posts.

[awesome_dude]

A friend of mine once told me - learning a new field is all about learning the language of that field

[jiggawatts]

What they hear:

"Exorcise the lattice hoard to siphon the new incarnation."

What we said:

"Purge the web cache to download the new version."

[lukan]

That metaphor would here be pretty accurate, though.

[BobaFloutist]

I think that's probably not an accident.

[macintux]

A friend of mine asked me why we have such precise terminology in IT; I asked her why English has so many different words for "chair".

[eru]

That's a big part of it, but far from everything.

[awesome_dude]

I'm not really sure - I deliberately stopped there because the concepts related to that field are a part of the language learnings.

[eru]

If you are a really big fan of something, you'll get familiar with the lingo, but that doesn't mean you can play StarCraft well or weld or shred your guitar.

That's actually part of why FizzBuzz was so notorious: there were (apparently) plenty of people who could talk the talk about programming and software engineering, but couldn't do FizzBuzz.

[awesome_dude]

You're right, people write code all day long and have no idea what pattern it is that they've just applied.

Having said that, they cannot communicate that that's what they want done, nor can they receive instructions to do something that way.

They really are hand in hand.

[Nition]

There was enough there for me to get the basic idea, which is fine I think. Can't really expect every niche post to have all the details necessary for a general audience and it's fun to get a glimpse into these worlds anyway.

Thanks for sharing the post!

[aa-jv]

I just love the fluent use of terms, and the whole ontology of the subject itself just seems so appealing to me. For a moment, I felt like others feel when listening to me and my colleagues discuss kernel build issues or other software challenges - befuddled, bemused, enchanted.

I guess, if/when I retire to that remote mountain hideaway, I might just get into this hobby. The idea of grinding my own mirrors to look at dew on the spiderwebs of the neighborhood is just so appealing.