Hack Chat Transcript, Part 1

A event log for Microscopy Hack Chat

Let's get small

Dan MaloneyDan Maloney 06/23/2021 at 20:070 Comments

Dan Maloney12:00 PM
OK, looks like people are checking in now, so let's kick things off. Welcome to the Hack Chat, I'm Dan and I'll be moderating today along with Dusan. Today we're excited to welcome Zachary Tong to the Hack Chat -- you've probably seen some of his cool stuff on the Breaking Taps YT channel. Today, we're going to focus on microscopy, though. See what I did there?

Dusan Petrovic12:00 PM
Hello and welcome!

Dan Maloney12:00 PM
I'm not sure I've seen Zach log in yet, though. Are you out there yet, Zach?

polyfractal12:01 PM
Heya! This is Zach / Breaking Taps. :)

Dan Maloney12:01 PM
Oh, that's right -- forgot about the @polyfractal thing. Sorry!

Hexastorm12:01 PM
I looked at the laser microscopy video, it is amazing. You showen how easy it is to make.. still have you considered moving a prism or galvo to move the laser bundel?

polyfractal12:02 PM
Hehe yeah sorry, I'm "polyfractal" pretty much everywhere except on my YT channel :)

Dan Maloney12:02 PM
Can you get us started with a little about your background?

Timo joined  the room.12:03 PM

Lageos joined  the room.12:03 PM

polyfractal12:03 PM
Sure! I typed up a little background before-hand.

So my background is actually in biology, which might be a surprise for folks that have seen some of my videos. Or maybe not, considering my poor engineering/EE skills hah. I have a degree in cell bio and worked in a wet lab for a number of years (culturing kidney and primary hippocampal neurons, running assays, etc). However for the last 10 or so years I've been in software. Most of that time working on the analytics functionality of a search engine called Elasticsearch.

Anyhow, I started my YT channel when I picked up metalworking, and it's slowly morphed into material science and microfab stuff. As my projects have gotten "smaller" over time, I keep finding myself needing (or wanting) new ways to measure/quantify the projects. Which has led to a proliferation of microscopes in my shop :)

To date, I have a few optical microscopes, a DIY laser confocal, a DIY "macro" atomic force microscope, a real AFM and a raman spectrometer. Contemplating building a chromatic confocal next, or maybe a white light interferometer. Definitely enjoy building instruments, even if they don't end up quite as useful as the real commercial ones :)

Peter Braubach joined  the room.12:05 PM

polyfractal12:06 PM
@Hexastorm Thanks! Yeah, considering some options to speed it up if I ever do v2. A galvo seems like a good approach, and you can get them pretty cheap (metal etching fiber lasers use them, so they are relatively mass-produced and cheap). A bunch of folks suggested CD/DVD optical units as an option too, which basically has all the guts pre-built and you just have to interface with it

perlsackhd12:06 PM
Are you planning on realeasing the code for your LSM?

morgan joined  the room.12:06 PM

polyfractal12:07 PM
@perlsackhd I wasnt originally but a bunch of folks have asked, so I'm currently compiling to throw on github somewhere. Need to find a RPi that i've temporarily misplaced :) The code is quite poor though, just quick bodges to get it working and interface with OpenFlexure (i hacked a new endpoint onto their server code)

Dan Maloney12:07 PM
A couple of links for reference, in case you haven't seen them:

Dan Maloney12:07 PM


3D-Printed Laser Scanning Confocal Microscope Measures Microns

When one thinks about microscopy, it seems to be mostly qualitative. Looking at a slide teeming with bacteria or protozoans is less about making measurements and more about recognizing features and describing their appearance. Not all microscopes are created equal, though, with some being far more optimized for making fine measurements of the microscopic realm.

Read this on Hackaday

Dan Maloney12:08 PM


Macro Model Makes Atomic Force Microscopy Easier To Understand

For anyone that's fiddled around with a magnifying glass, it's pretty easy to understand how optical microscopes work. And as microscopes are just an elaboration on a simple hand lens, so too are electron microscopes an elaboration on the optical kind, with electrons and magnets standing in for light and lenses.

Read this on Hackaday

Hexastorm12:08 PM
@polyfractal you should check out my video, I have a laser scanner with a fpga . Actually after seeing your video I thought of adding reading

polyfractal12:09 PM

polyfractal12:09 PM
sorta followup on the v2 subject, one variation I'm considering next is a "chromatic confocal", which scans the full Z-stack simultaneously. It's a really clever setup which "abuses" chromatic aberration to determine the height. They are considerably faster than regular confocals if you don't need fluorescense, etc and just want heightmaps

polyfractal12:10 PM
@Hexastorm will take a look after, cheers for the link!

Lageos12:10 PM
Ist it possible with the your icspi afm to take force curves to get local material parameters?

Dan Maloney12:11 PM
That's really cool. What special about the "specially designed lens" - designed to maximize chromatic aberration, I suppose?

Nicolas Tremblay12:11 PM
Doesn't the chromatic confocal get influenced by the color of the sample?

Hexastorm12:11 PM
@polyfractal project is here ... you should also check out the startup they have an interest in your work and use light + ai to detect biomarkers, anyhow enough promotion 😉

polyfractal12:12 PM
@lageos I _think_ it can take force curves (i saw mention in the manual) but to be honest I haven't played with it yet so can't really say much else. I think it's part of the advanced config/settings i haven't really touched yet

perlsackhd12:13 PM
@Dan Maloney The lense is needed so that the diffrent Wavelengths have diffrent focal distances

polyfractal12:14 PM
@Dan Maloney Yep, pretty much. I think they are known as "hyperchromatic" lenses, but i believe you can also stack up a bunch of spherical lenses and stretch out the colors

polyfractal12:15 PM
@Nicolas Tremblay yeah, my understanding is that some of the "special sauce" in the commercial units is the software that helps determine when it sees a peak, since color does affect the absolute amount returned. but in theory with a good spectrometer and some intelligent thresholding you can work around it. Nanovea and the other companies claim it works on all colors and reflective so there's _some_ way to do it

polyfractal12:17 PM
@Hexastorm that's neat! Definitely going to have a closer read. I'm noodling over a direct write laser lithography system in the future so this would be good reading for that too :)

Nicolas Tremblay12:17 PM
Ok, so the error correction is mostly on the software side with a bit of pre-filtering.

kjansky112:17 PM
I'm surprised you haven't delved into a self hacked SEM.

polyfractal12:18 PM
yeah, that's at least how I've interpreted it based on some papers and noodling over the commercial units marketing material :) but i'm sure the devil is in the details, as I learned with the regular confocal hehe

Thomas Shaddack12:18 PM
Random thought. Confocal microscope, using two-photon process for curing photoresists with resolution quite below the diffraction limit.

Dan Maloney12:18 PM
Read that as *curling*, was confused

Thomas Shaddack12:19 PM
if the resist is curling, your adhesion to substrate sucks. :P

polyfractal12:19 PM

polyfractal12:19 PM
@kjansky1 yunno, I keep wanting to (there are some cool papers for mini SEMs using permanent magnets!) but tbh my EE skills are terrible, and HV scares the daylights out of me. Slowly working on learning more because I'd love to, but yeah, the electronics part is my nemesis. Really want to work on a focussed ion beam even more than SEM actually, but same issues

Thomas Shaddack12:21 PM
The danger of HV depends more on the deliverable current (and energy). You can get dozens to maybe hundreds kV from static spark. It's the current that kills, the voltage only pushes it through.

Birk joined  the room.12:21 PM

Ahron Wayne12:21 PM
And then to be even more specific, if you have a high voltage across your body, you will also have a high current going through it too. V=IR is always always always true.

Hexastorm12:22 PM
@polyfractal , have you ever considered laser induced forward transfer? would be curious to see a simple setup

polyfractal12:22 PM
good to know! actually on that note, if anyone has recommendations on HV texts/tutorials/etc I'd be grateful! Sometimes hard to find good learning resources that aren't like "Build a tesla coil!" style resources

Ahron Wayne12:22 PM
Also I just wanted to comment that it's cool you have a bio background before this. I started in biochemistry and the transition to engineering was interesting to say the least.

Thomas Shaddack12:22 PM
Depends on how "hard" the power supply is. If it is weak, the voltage quickly drops.

kjansky112:23 PM
Read somewhere of a hacked SEM with a reworked gun from a old CRT for the beam.

Nicolas Tremblay12:23 PM
For HV, go look up Plasma Channel. He might help you

Hexastorm12:23 PM
@polyfractal how long did it take you to make the laser confocal video (excluding construction) ?

Dan Maloney12:24 PM


Into the Plasmaverse Hack Chat

Jay Bowles will host the Hack Chat on Wednesday, September 23, 2020 at noon Pacific Time. Time zones got you down? Here's a handy time converter! Most kids catch on to the fact that matter can exist in three states -- solid, liquid, and gas -- pretty early in life, usually after playing in the snow a few times.

Read this on Hackaday

Spida12:24 PM
Anybody here knowledgeable about DIC (differential interference contrast), especiallyin the reflected light variant? how does the choics of a DIC prism depend on the lens?

Dan Maloney12:24 PM
We had Jay on last year!

Nicolas Tremblay12:24 PM
@Dan Maloney , yup, that was a fun one :P

polyfractal12:24 PM
@Hexastorm yes! I love that you know of the technique, it's super cool. I've tried a few times but haven't had a lot of luck getting "clean" transfer. just molten splatter, or complete vaporization. Part of the issue I think is the laser software -- the literal worst software ever made, EzCAD -- which makes it hard to precisely control the beam. E.g. hard to drop a single pulse where you want it. But I think it should be doable with a bit more tuning, it's pretty trivial to get "large" transfer like copper from one slide to another

a.uebener joined  the room.12:24 PM

polyfractal12:25 PM
Will check out Plasma Channel, thanks!

polyfractal12:26 PM
@Ahron Wayne yay another bio! Yeah I imagine transferring into a real engineering role would be quite a change :) Software was a decent side-move for me since I always did software stuff on the side (originally was a CS major)

polyfractal12:27 PM
@Hexastorm like just the filming/editing part of the video?

Hexastorm12:27 PM
@polyfractal yes

Thomas Shaddack12:27 PM
I did some experiments with control of a CO2 laser. Notoriously hard to get low power from the tube, the discharge won't light/stay at low currents. but the power supply responds *fast* so the amount of energy delivered can be easily controlled by the pulse time, which is easy to generate with a spare timer on the arduino with just a bit of patch of Marlin.

perlsackhd12:27 PM
@polyfractal What project would you recommend for a beginner who wants to dip his toes in diy microscopes?

polyfractal12:29 PM
gotcha. Filming is typically a few hours tops. I like to just let the camera roll and do takes until I'm happy with the delivery, then move on to the next section and repeat. Afterwards grab any b-roll as required. Makes editing longer though since there is like 2 continuous hours of footage to work through. Editing is probably 5-6 hours total, plus thumbnails and all that jazz. but yeah after a project is "done" i can usually get the video part done in a weekend'ish

Birk12:29 PM
Uhm... So that's it? Just a bunch of people chatting?

Uwe Kackstaetter joined  the room.12:29 PM

Ahron Wayne12:29 PM
That would be the case if I was ever in a "real" role, still goofing off in an academic setting :) I have considered being in software just because it's so in demand and it's accessible for work. Not sure if my Python skills are good enough for a "real" job though.

@perisackhd I would recommend you start relatively macro, like with a USB microscope or RPI lens flipped backward. Or you can work with an existing project like openflexure.

polyfractal12:30 PM
@Timo afraid I don't know much about how DIC works, only used it as an end-user in lab :(

Ahron Wayne12:30 PM
@polyfractal did you have a "big break" when it came to making videos, or did you have a steady clip of subscribers from the beginning?

polyfractal12:33 PM
@perlsackhd ++ what @Ahron Wayne mentioned. OpenFlexure is a pretty great little ecosystem. Or just hooking a microscope objective up to an RPi camera yourself, the simplest form is just an objective + camera. Make sure to get a non-infinity objective, they are typically around 160mm. meaning the camera just needs to be 160mm away. The infinity lenses are focused to infinity which is great when you need other stuff in the optical stack (like beamsplitters, etc) but complicates things since you'll need another lens to focus it onto the camera

Dan Maloney12:33 PM
@Birk -- that's why we call it a "Hack Chat"

Nicolas Tremblay12:33 PM
Open flexure seems like a great start to get into "optical" microscopy

Dan Maloney12:33 PM
Feel free to join in with questions, though

kjansky112:34 PM
How about something like this: Fiber-optic confocal microscope using a MEMS scanner and miniature objective lens

HJ Shin, MC Pierce, D Lee, H Ra, O Solgaard… - Optics …, 2007 -

polyfractal12:35 PM
@Ahron Wayne definitely had a "big break" moment. I was slowly accumulating subscribers up until about 5-6k, then the YT algo decided to push a ton of traffic to my high speed chatter video and that really blew up the subscriber count. Ben Krasnow also noticed the copper deposition video and tweeted, which brough in a lot of cool folks :)

Ahron Wayne12:35 PM
@perlsackhd and not to gotcha @polyfractal but if it's non-infinity, it doesn't have to be *exactly* that distance away (something I worried about when I got into macro). If the lens is closer to your sensor the image will just be less magnified.

polyfractal12:36 PM

Ahron Wayne12:36 PM
@polyfractal I indeed first saw you through your high speed chatter video. 5-6k is still really great to me too.

Dan Maloney12:36 PM
Cough cough, Hackaday ;-)

polyfractal12:36 PM
that's actually one thing i like (and sometimes curse) about optics, there's a lot of manual fiddling/tuning you can do to get things working. and it's relatively accessible since you can stick a piece of paper in between lenses to see what's going on

Dan Maloney12:36 PM


Analyzing CNC Tool Chatter With Audacity

When you're operating a machine that's powerful enough to tear a solid metal block to shards, it pays to be attentive to details. The angular momentum of the spindle of a modern CNC machine can be trouble if it gets unleashed the wrong way, which is why generations of machinists have developed an ear for the telltale sign of impending doom: chatter.

Read this on Hackaday

polyfractal12:36 PM

polyfractal12:37 PM
:) <3 HaD

Dan Maloney12:37 PM
Think that was the first time I had seen one of your vids, actually, so it probably was that mysterious YT algo push.

polyfractal12:37 PM
and yeah, I was pleased as punch at 5-6k! didnt know what to do with myself when it like tripled in a week :)

polyfractal12:38 PM
the YT algo gods move in mysterious ways

perlsackhd12:38 PM
@polyfractal I too saw the chattering video first then long time nothing and after seeing the LSM video remembered the Chattering video

Ahron Wayne12:38 PM
What is a video that you worked really hard on, or just otherwise wish got a lot more attention?

polyfractal12:39 PM
@kjansky1 just had a quick skim, that looks really neat! only downside is that fiber stuff can sometimes be expensive, but it does remove a lot of the alignment issues too which is great, and the fiber itself acts as the pinhole, etc etc

lilykorea9 joined  the room.12:39 PM

lilykorea912:39 PM

lilykorea912:41 PM
i need help plss

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polyfractal12:42 PM
@Ahron Wayne hmmmm, good question. I have a soft spot for a video about hollow microlattices, sorta based on a Science paper, which for various reasons didn't do super well (at the beginning of my transition to material science topics, too much faffing around in the beginning, etc). but I thought it was a neat topic :)

More recently I did a video about sputter shadow masks, but included a Blade Runner trailer spoof and was too cutsey with the title/thumbnail which really penalized traffic. oh well :)

polyfractal12:43 PM
obligatory hackaday link to save Dan having to go digging for it :)