DIY Scanning Laser Microscope
HTML-код
- Опубликовано: 12 май 2024
- CONSIDER SUBSCRIBING 🥰
☕Buy me a coffee? www.buymeacoffee.com/Breaking...
🔬Or Patreon if that's your jam: / breakingtaps
📢Twitter: / breakingtaps
💻Discord: / discord
I built a 3D printed, scanning laser confocal microscope so I could collect 3D surface topology and profilometry data! The microscope stage is based on an OpenFlexure "Delta" stage, and the confocal optics are constructed with a 3D printed body, some lenses, a 405nm laser, pinhole and photodiode. The microscope is controlled by a Raspberry Pi (which controls an arduino to move the steppers).
It's not beautiful, it takes forever to scan, and the images are of dubious quality... but it works!
OpenFlexure: openflexure.org/
0:00 Intro
1:56 Confocal vs Widefield Microscopy
3:25 OpenFlexure Motion Platform
4:01 Confocal optical breakdown
8:00 Delta motion stage
8:43 Photodiode amplifier
9:14 Confocal Pinhole demonstration
10:31 Camera vs Photodiode
11:31 Data processing considerations
14:05 Images and results!
18:22 Optimizations
21:37 Discord! Come hang out with us! 
Наука
Dude your videos look soooo good. Also, sweet microscope :)
*Videos shot with a confocal laser microscope*
❤ Thanks! Don't tell anyone but I only release videos because I like color grading footage and pretending I'm Michael Bay. All the science junk is an elaborate cover story 😇
@@BreakingTaps where's the explosions then? bay movies are 50% explosions minimum!
@Herr Gerd Soon™ hahaha
Since you're here, and your most recent video is weeks old and has tens of thousands of comments :P
@Stuff Made Here: Idea for you: A holster for cops that when the firearm is drawn it automatically calls for backup and EMS. Beau of the Fifth Column did a 9 minute video showing some of the benefits of it.
Either try to make one yourself, or help put out the message that this would be good for cops and the people they point firearms at.
I have absolutely zero need for a "confocal laser microscope" but your channel is so incredibly well done I can't help but watch.
I'd love to have confocal laser microscope but I need it so little that I cannot justify even the cost of DIY project to get one. Just like I would want to have accurate spectrophotometer, too.
I've never heard of one but now I need one
It's one of those impulse buys frfr
What's this, I see laser but nothing getting burnt, evaporated or even slightly charred? 🤨
JK that's really cool and I am looking forward to that thing back there in the summer!
Nice to see you here. Guten Tag!
okay, break time's over. Go work on OSMU some more.
Just _really tiny_ charring on the sample 😉
So fun to always see my most loved youtubers on the same channels I subscribed to 😄😄😄
Well we all like Science 😄
why are you browsing RUclips videos? Don't you have a CNC mill to be recording for us?
Very cool. In the 1990s I worked with a startup developing a commercial confocal laser review station in the semiconductor industry. We scanned the laser in x-y and had a piezo stage for the z-axis. It also required a proprietary frame grabber board that was synced to the laser scanner and z-stage. My work was on the microcontrollers, so I only knew the general optics design. We experienced what we called the pit-particle issue where what we knew to be a solid above the surface (a sub micron calibrated latex sphere) could sometimes show up in the 3D image as a hole.That seems similar to what you were sing on the one image. Our optics engineering team spent a lot of time resolving that, but I don’t recall how they attacked it. Great video. Thanks.
That seems like a problem that could be "solved" (mitigated maybe) by analyzing the curve. If the peak is out of reach there should be a steady climb before, which should be detectable with a proper numerical analysis. Then I would replace this value with a max value. It would at least make it obvious in the image where the 'z cropping' happens, instead of random valleys.
If I may suggest - please consider putting the transimpedance amplifier _very_ close to the photodiode, preferably mount the diode directly piggybacked on the opamp IC (directly soldered, no sockets) onto the DIP8 of the opamp. The capacitance of the long coax between the PD and the TIA limits the bandwidth, in your current setup.
Yep. And also using a smaller diode will give better speed (thx lower capacitance) and lower noise.
Cheers for the tips! This project really taught me that my EE skills are terrible and I need to spend some time learning the fundamentals. Just barely got the amp working and it really is awful in every way :) Will keep that in mind for the next one, I forsee myself needing a decent photodiode amplifier in the future :)
I think one of the reasons why you're getting artifacts is because of how metals reflect light : it's mostly specular reflection(it's directional, in your case parasitic) and not diffusive (unidirectional, what you're detecting). metal oxides, however, tend to build up in tiny crevices of metal surfaces and they are dielectrics, so they create tiny diffusive areas in otherwise specular metal which might look like noisy height changes.
This is a bugaboo when working on PCB's under a microscope generally. They are SHINY, and what you see is not a nice illuminated surface but a reflection of the light source. That's why we use ring lights to work on PCBs, at least that eliminates reflections from the surface plane, although not from solder fillets.
I think you are right about reflections. And to add something else. I think some reflections are courses by lights other than the laser. Like the image with the "EC". The left, white part of the image could have a lot of room light. Then the lights were turned of for a little while. And then a small light in the room is turned on what causes the reflections on top of the characters.
But I could be wrong because the scans took multiple days and then I would expect to see more day night effects.
@@Daniel-zw6gz What type of temperature fluctuation is seen in this workspace over 24 hours? The PCB has many components, each with a different CTE. Also conformal coatings can confuse the sense of sharp focus.
Egads! Sorry, this is not where I should have put the question!
I was thinking about reflectivity, too, after a recent experience trying to use photographs to create 3D models using Meshroom. Reflections make it basically impossible for the algorithms to figure out what's going on in the images. Anything reflective has to be dusted with a matte powder to get it to work.
For small movements like, that, maybe a voice-coil based actuator would probably be better - could you maybe adapt a CD/DVD optical block?
Piezo will also be nice, voice coil need some clever close loop thing which piezo you can almost get away with complete open loop
Agreed! Would be a _ton_ faster and probably more precise too. Lesson learned I suppose :) There's a followup technique (chromatic confocal) which I might explore, and will definitely explore alternative motion options. The OpenFlexure stage was super convenient but I didn't realize the movement speed itself would end up being the limiting factor.
maybe heads drive from hdd drive could be better?
really awesome project!
i think you should use kinda white matte spray paint to get rid of scanning artifacts.
i've build ultrasonic "scanner" to make an image using standard arduino us-sensor and had a lot of time to figure out what do i see on my result images )
That is what I am using and you can scan thousands of points per second. I only have dvd lasers on hand but you get better resolution with a BluRay laser. You also get the entire optical unit and sensor as 1 piece and only need to build the stage. There is also a chip inside the drive that contains 7 op amps / comparators to control the voice coils and time the readings.
After watching this video, I thought this was going to be one of those huge million plus channels that I just hadn't heard of yet. That you only have 25k subs is outrageous to me. Everything here is on par with the best of the best RUclips has to offer.
You could try to have the beamsplitter at the Brewster angle of you laser source and mirror material, could avoid the laser dump, when the optical path is geometrically redesigned.
Woah! That's new to me, just did some reading. Very cool! I had no idea polarized light had that property.
@@BreakingTaps brewster's angle is the kind of thing when you see it happen, the coffee goes out your nose
even if you're not drinking coffee
@@GeorgeTsiros This comment caused coffee to come out my nose. And judging by my neighbor's shouts, I know from where the coffee was teleported.
@@BreakingTaps There are two more reasons for the poor SNR: (1) the laser beam is highly aberrated due to poor alignment quality, and (2) some reflected light will be fed into the laser cavity, which actually affects the output beam intensity. The reflected beam is definitely something you want to avoid.
If the laser is polarized, it might be an option to filter the returning light in that direction to exclude specular reflection from those shiny surfaces. That reduces the return signal very much, but scans for scattering and the surface geometry matters much less, which may otherwise deflect a focused beam in a different direction. It has the same effect as coating the surface matte.
If you're still working on this, consider replacing your photodiode and aperture with a linear CCD array. You can use the reflected beam width as feedback for the next Z position to find the focal height in 2-3 iterations instead of scanning.
Dude your video quality and experimental setups keep on getting better! Awesome stuff, keep it up!
Thanks! Really appreciate it :)
Really cool project! Another way to do this is by using a standard cd or dvd laser head. You cannot scan very large areas, but with very high resolution.
Thanks, and cheers for stopping by! Will take a closer look at those DVD units, are there open source designs/plans/software to control them? I'm not sure I have the skills to hack one myself :)
@@BreakingTaps I think that styropyro has some tutorials on youtube, and they mostly revolve around an lm317 regulator. Also I had an idea for the optimisation which might be interesting: set a grid over the area you're scanning, and go to each point sequentially and move the z axis to find the height of the point. After the first scan look for areas where there is a large change in height and then go back to get more resolution in those areas. This should result in being able to start with a coarser grid which should make the scan a bit faster, although fine detail may be lost in some areas. This was really cool and I don't need a confocal microscope but now I'd really like to try at some point
@@BreakingTaps They are actually not that difficult to control. But, one potential problem is that you need a special 2x2 photodiode to focus properly.
Let me try to explain: imagine a 2x2 grid of photodiodes, with them being oriented at 45 degrees. The optics in there are special so that if you are too far away, the beam becomes elliptical from top to bottom, so the top and bottom photodiodes get more light than the left and right one, but if you're too too far away, the left and right ones get more light than the top and bottom ones. And if you're perfectly in focus, the laser for forms a perfect circle and all photodiodes get the same amount of light. I know Hamamatsu offers photodiodes that can be used for that, but they'd probably cost you a kidney, and the chip that's currently in there doesn't expose the focus data to you. If you want pictures for what I'm talking about, wikipedia has images in the article about the CD player.
But driving the coils themselves is relatively easy, their movement is proportional to the voltage across them.
Actually, a laser unit should be a pretty good confocal stage if I'm not completely mistaken, since you have the exact same thing happening that's happening here, and it's all one unit.
@@BreakingTaps dude there are absolutely tons of wonderfully documented open source projects utilizing the high end opto-mechanics in a standard DVD/Blu-ray optical pickup.
a bit of googling, there are a few things on hackaday and elsewhere. Really incredible documented projects out there.
One of my favorites will show up in Google image results… You will see a nice looking finished product with all of the circuitboards in a purple color. They got some really good results with that, and I think A set a fresh eyes like yours could really push the project further.
Billions of dollars of R&D have gone into developing the optical pickups in some of the higher end units. They absolutely engineered those things to within an inch of their life 😂
I’ve got dozens of them, so if you need some parts just let me know and I’ll ship you a box no charge. Also have a bunch of really high-end hamamatsu optical sensors and components from a bunch of equipment I’ve repaired or salvaged. So I may just have something you need. I’ll gladly chip in and help however I can
I need (want) one!
Awesome work, man!
Jesus christ! this is a 2Msub channel level production quality! how you manage!
I mean, i loved all your videos but you really outdid yourself with this one!
This is really well done! I watched an OpenFlexure video and this was suggested. Really shows that a lot of time went into the project and into the presentation. Wishing you the best of success.
Thanks Kent! Good to see you, hope things are well!
Awesome stuff! I'm amazed that the data collection was actually limiting - I probably would have gone with a different xyz stage and scanned voxels one by one and been way too slow. the continuous scan seemed to be enabled by the latency of the stage so that's pretty awesome! I'm also glad you called out the big cylinder of conflat flanges in the background cause I was getting really curious...
Thanks! Hehehe, I'm pretty excited to start working on the chamber, think I have all the necessary components... just need to wait for my garage to warm up a bit (we just got more snow! argh!) and machine a few different adapters. Soon!
I'm only slightly surprised to see you here
It's just a matter of time until this channel explodes. Keep on!
I think the biggest issue is the range of reflectivity. I had this issue with 3d scanning using photogrammetry. Your photos will be greatly affected anywhere there is solder on that PCB, or other curved highly reflective areas. It might be worth trying to air brush a flat color on everything to make the reflective properties uniform, which should normalize your readings and greatly increase the resolution and accuracy of your photos. If air brushing adds too much material to the sample, there might be some gaseous coating options like 2D boron nitride that would only add 1 atom to the height. Good work though. Your channel will do great :)
This man is absolutely incredible. I wish I was able to retain and use learned information as well as he does. He just is a wealth of knowledge.
You retain information by using it. Memorization is a myth and not real learning.
That project deserves a subscription right out of the box ! Thanks for producing such an interesting content.
There should be a tech/science youtuber collab, you'd fit in nicely!
Sounds like something Hank Green (SciShow, Crash Course, Journey to the Microcosmos, etc etc etc) could be interested in... but no idea how to get his attention.
Hey, I make confocal, whitelight interferometers and microscopes for a living. Here is a few insights to improve your results.
1) Your setup is non-rigid, which means there will be vibrational motion and modes oscillation between sample and microscope.
Fix this by adding a heavy base and using steel instead of aluminum.
2) Laser Diodes suffer from Speckle noise, which is up to 15% of intensity. Switch instead to a LED based emitter.
3) Dont leave cables hanging, air drafts might push and move source or detector. Make sure they are fixed.
4) Using thick half mirrors is not recommended, as they create ghosting. That happens when double reflections overlap with slight change in angle. Cheap option is film beam splitter or cube beam splitter.
5)In Confocal, we dont move the stage to scan. Instead, we use DLP (mirror arrays) or liquid crystal to raster the image, pixel by pixel at a fixed height, then move along Z, until we find the peak for all points.
Otherwise, its a cool prototype V1. good job.
Awesome, thanks for the tips! Really appreciate it! And doh, didn't even think about the detector moving but that seems very obvious in retrospect. Interesting about DLP, I assumed commercial systems used a galvo system to raster the laser around. Very cool, thanks for sharing!
This channel just keeps getting better!
You've come such a long way in your video production. Hilarious intro and great quality, plus intriguing topics!
Hey, awesome video! I see there already was some comments about reflective surfaces here - and that is indeed the probable cause for the inverted shield structure. When the beam hits the slightly higher point of the shields edge it is scattered into the room and not back into the lense making the signal weaker. This would explain the smaller values in some of the curves peaks too. Alexander Sannikov mentioned in their comment that the metal oxides being diffuseve cause noise in the signal. Indeed if the samples were to be prepared beforehand (like they do for electron microscopes) to be compleately matt with a coating of a white matt substance the laser would behave more uniformly along the entire surface.
This is amazing! It's fantastic that you can achieve this level of detail using 3d printed components. The explanation was very useful and covers a topic which isn't well covered elsewhere. Thank you.
Very cool, i worked on a similar project a few years back using DVD optical pickup heads and its internal optical path, which is indeed a confocal arrangement with an electromagnetic vertical adjustment which provides a high degree of precision.. my failure was in the X-Y stage.. might have to revisit with openflexure but it was something that worked as an arduino shield.
2 minutes in, this is what it's all about on so many levels. So impressed already!
Fascinating. Great job and good explanation of the optical path. I wonder if it would be faster to run the scan like an atomic force microscope, riding the surface by tracking the amplitude of the photodiode. Move a step in x, then move the z up or down to maximize the amplitude, repeat. Advance y each time you hit the end of x. The assumption is the surface is often flat, or at least has a gentle slope, so instead of scanning the whole z stack for an x,y point, just search around the last height (z) each time you move to a neighboring point.
I would think you could then attempt to recognise the trend from previous points in the direction you're currently moving and predict which way you need to scan in z.
Cool project. Try to modulate ur laser beam with chopper or so and demodulate ur photodiode signal at the same frequency. This will remove much of noise.
Good point! I was about to suggest some physical wavelength filtering as well, just to remove signals from ambient light, but some decent modulation will remove a lot of the ambient (DC in any case)
Did a fair amount of optics work in university and self-taught myself analog electronics using photo-diode amplifiers. One of my best had a 60fW noise floor, saturated at 20nW, 10Gohm trans-impedance gain, and about 30Hz bandwidth. Very slowly working on a V2, but happy to share V1 in the mean time.
Please do, a pic of a hand drawn schematic will already give people a direction to follow. Make a blog or RUclips post and eventually Google will find it.
I love the presentation and the work! It was fun to see bits of it in development, and it came out beautifully.
Very cool! My knowledge of optical scanning goes no further than end user where I push button and machine goes brrt, so it's great to see the community come together with advice.
I'm very excited to see an upgraded model!
Wow!
Really interesting project. Hope to see more of this soon. Thank you for sharing!
Phenomenal video and experiment/build quality. Your presentations have the perfect amount of technical info, and I love hearing about the mistakes/troubleshooting. I hope to see your channel grow and can't wait for your next video.
Super interesting project! It blends my love of making and metrology. Looking forward to seeing more videos!
This is really impressive! It's great to see people really pushing the limits of DIY science.
I love the way you explain! Thank you for shining the light of knowledge all over like that.
The curved surface at the top of the shield is probably scattering light like a convex mirror. If you had a matte textured object you might get better results.
Your channel is *insanely* underrated. This is sooo cool.
Wow this is the best channel! BT, great stuff as always! If it doesn't mess with your workflow too much you should consider discussing the upcoming projects at the end of your videos. Also, I'm sure you run into a ton of problems trying to get these types of amazing things working, you should consider asking for help (suggestions and ideas) in the comments. It would help with the RUclips algorithm, it would get people emotionally invested and it would help you make more videos. Apart from the obvious, I think one of the biggest reasons that AVE and Applied Science have been so successful is that they spend a lot of time fostering genuine discord in the comments. Great videos!
That's a good idea, just might start doing that! One thing that makes me hesitant is that I'm never _quite_ sure what projects will end up working out. E.g. I have a few being worked on right now, but it's pretty common for a project to hit a roadblock and pause indefinitely (the confocal was nearly at that point, before I had some ideas to fix the problems). I'd be potentially worried about sharing projects that will never get turned into a video due to circumstances. Think that would be a problem? I don't want to mislead viewers, but maybe I'm just overthinking things here? :)
But that's a good point regarding help - lots of smart people watch these videos and might be able to help me unstick the problem projects, so from that perspective it makes a lot of sense to share a little more proactively. Was just chatting with someone who wanted to see some videos about my failed projects, maybe I can do a somewhat recurring video about work-in-progress and failed projects, see if folks have ideas.
In any case, cheers! Appreciate the feedback! Will think over the best way to do that.
This is amazing. The intro and its high level editing took the video to places I would have never expected/seen from technical engineering youtube. It was a fresh breath of air. And how you explained the optical parts and what they did made things click that for specifically optics rarely do for me. I have never heard of the 3d printed micromover. You were already a contender for what I consider the absolute top of youtubers (Thought emporium, Tech ingredients, applied science, nighthawkinlight etc). This video cemented it.
I am curious if you will vary how you frame/edit your video or continue to expand on what you did in this video. Like If some future videos are similar to you earlier videos or not (I guess it depends on what project youre working on and heavily dependent on what you like at the moment)
Thanks! Really appreciate it! I admit the intro made me nervous to post, since it's a bit unusual for this kind of channel. But I enjoyed doing it and thought it was fun, happy to see other folks liked it too :)
Yeah I'm not sure to be honest, I think it's an evolving thing as I become more comfortable filming and editing (and being on camera myself). I think I probably won't do many more of the "film a whole bunch of timelapse machining" anymore, since it's both a lot of work and not as interesting in my opinion. I'd like to keep doing "creative" stuff, but also want to make sure I keep the technical/science content prioritized, so it'll probably be a line to walk depending on the project and content. E.g. I have a few projects in the work that would probably fit more creative filming, and others that would probably benefit from a dryer presentation.
As to actual content, definitely all over the place :) I'm going to try and keep it roughly in the bounds of optics, material science, nanofab and machining-adjacent just so viewers sorta know what to expect. But I have a lot of interest in those fields so it'll probably wander around as my ADD brain changes course :)
Great video, 20 minutes fly by, just the right level of detail. From my experience stacking microscope shots and focus failures, it will be that 'specular highlights' (very shiny surfaces) break your algorithm. You'll be assuming that the thing you are scanning has unchanging topology (which is true), but accidentally assuming that when you move the microscope stage that the pattern of light reflected would not change (untrue), because unless the surface is perfectly matte, the 'brightness' does not 1:1 correlate with 'in focus', it also correlates with 'shiny thing pointing at lucky angle to send light back to sender'. Imagine you were scanning a microscopic disco ball, if you strapped a torch to just above a camera lens and moved it closer and further, you'd see that different panels would suddenly become very bright, and others very dark. It confuses normal cameras with their contrast based focus detection (and even sometimes phase detection). If you want to test what I'm talking about, scan some glitter or a retroreflective tape.
I would spray the item to be scanned with a misting of 'airplane glue' smelling hairspray in the giant cans from 50cm away. It will 'matte' your surfaces sufficiently. If it kills the retroreflection of tape, it will be scannable by your algorithm.
Man! your videos are awesome. We get months worth of education in science and technology in every one of them. Your detailed way of explaining is incredible. Thanks
This was a great video. I've found having a fiberoptic cable act as the pin hole to be a good solution. Also adding 2 scanning mirror to traverse the XY plane reduces the need to rely on mechanical movement. A photo-multiplier-tube is a great way to increase the electrons per photon ratio. Also using a quarter wave plate and a polarization beam splitter lets you keep more of the precious photons going to the source.
Interesting, I had thought about using a fiber but wasn't sure if that was correct or not. Does it have to be a single mode fiber, or would larger multi-mode fibers work too? I guess larger would be fine, since I'm already using a multi-mode laser and I should care one way or another anyway. Might give that a shot!
Good idea about quarter wave and polarizing beam splitter! Looks like I need to grab a few more optical components to have on hand for the next project :) my box of optics is slowly growing haha
@@BreakingTaps - MMF is more forgiving because it's 50µm vs SMF being 10µm. Either is a PITA for alignment / focusing. I think going w/ some wave plates and polarizing beam splitter would be more useful to keep those precious photons going to the meter. Good luck!
The quarter wave plate and polarizing beamsplitter also reduces optical feedback into the laser diode. Optical feedback into a laser diode can cause a lot of noise.
Using single mode fiber gives a smaller effective pinhole and a diverging beam that can then be well collimated with a single achromatic lens, which would remove the need for the input lens in your beam expander. I have just butt coupled a telecom patch cable, with a 9 micron diameter core, to a high power LED and imaged the output onto a cheap security camera and have to turn down the current to the LED to not saturate the pixels on the camera. If you need more power into the fiber, you can buy a "visual fault locator Fiber optic cable tester" which couples mW of light into the core of a single mode optical fiber with no alignment. These are available on Amazon for under $20.
You could also use a fiber-optic circulator or a 3dB fiber optic coupler to replace the beamsplitter, which would remove all need to align pinholes to precise locations.
@@bretcannon3826 That Y coupler is a brilliant idea. The optics would be one focus lens to bring the fibre end to a parallel beam for the microscope optic. a fibre coupled laser and detector would complete the capture system.
Since the system determines depth based on intensity, maybe build a closed loop controller for the laser diode to ensure stability? Also get a bigger laser!
12:15 you can possibly increase the scanning speed dramatically by making a feedback system, like autofocus, which tracks the surface or, equivalently, the height at which the intensity is maximum, which is the maximum of the curve so when x-y changes, you need only change the z enough to stay at the maximum
Great idea. And if you can implement it with phase detection similar to SLR cameras, you don't need to even guess which way you need to move to get into focus. The end result would be pretty much like optical LP needle.
That said, laser scanner LP players do exist. Maybe one could take some ideas about those. I think the tech is old enough that the patents have already expired but are publicly available.
funny video ! It reminded me one of my internship : I had to build an interferometer to mesure optical elements with 10 nm accuracy for the Z dimension. But instead of laser I used a white light source.
Thanks for the video, it brought back some great memories :)
Absolutely love the jank to performance ratio of this project!
I'm floored. That was awesome. I finally have a project to pursue that will force me to crack the seals of signal processing, python, and optics. Thanks so much!
Goodluck! Happy to answer questions if you have any!
Reminds me of Ben Greer’s Single Pixel Camera that used Radon transformations to process the single pixel data.
YOU GIVE ME HOPE.
I'm in awe of this video. My intellect is only barely sufficient to grasp what the components do.
It's true that I feel bitter in myself for not being smart enough to do something like this. But I am profoundly happy that you are. It gives me hope for humanity's future that there are people as brilliant as you in the world. It really does. I wish you all the very best
This is really interesting stuff. I just finished my masters on the rotationally coupled imaging of spin coating using a similar optical technology for real-time surface topology observation of the process. If I were to continue I'd definitely integrate some of your mechanics!
i dont know how you dont have more views and subscribers, this is an awesome project!
Love the project! Miss doing this stuff. Man if it takes a week to image a surface you wonder how much temperature change over that time frame would impact the sample. Its a small area you're sampling but the whole object would chmage temp. For efficiency buildings can drop temp overnight. You're measuring such small features I wonder if it might be enough to cause some of those anomalies in the data plots. It's always a challenge coming up with the right algorithms to filter the way you want but not kill good data or pick the wrong point.
Love the project, great video, glad it showed up in my feed somehow!
Awesome work! Some vibration isolation might help with noise reduction. Air table would be nice but I’ve seen open source AFM and scanning tunneling scopes using a heavy platform sitting on balloons to decouple ambient room vibrations. Good luck! And thanks for sharing this with the world!
I cant even tell you how cool this is!
Thanks for sharing!
Great project ! For the data visualisation, you could try to display depth using color and intensity using opacity. This way you visually should attenuate the issue of incorrect local maxima. Use a color scale that has a constant luminosity like one of the cubehelix color scales
I audibly shouted "SIIIIICK" when you showed the topological renderings. Instant subscription.
I really can't stand how at such exhuming scientific and video quality you only have 25k subscribers. Luckily you have already managed to capture the attention of major scientific channels.
Awesome stuff!! The intro hit very close to home :D
I feel like every cool piece of instrumentation I see goes through the same cycle of realizing it's way outside my budget and then trying to decide how hard it would be to build :)
Super cool video! I actually deal with laser scanning confocal micros on a daily basis and its super impressive that you were ale to make one on your own, wow :D probably the next, more advanced step for speeding up the scans would be to use piezoelectric mirrors to deviate the laser beam instead of moving the sample. Also motorized lens in Z axis would be awesome to see :)
Wow!
That is really amazing!
Thanks a lot for sharing! Keep on going!
this reminds me of how old drum scanners worked, but i cant help but feel there is a better way of measuring depth (and over a much larger area simultaneously) while using a camera sensor and detecting image sharpness.
What if find particularily enjoyable about this video is that due to the relative simplicity of the optical setup it works really well as an explanation of how a confocal system functions. What you have built here is essentially a physical version of a diagram one might find in a textbook. The pinhole demonstration, for example, is really cool, since it's not something that you can show on a commercial confocal microscope, and the custom optical table-based setups are usually a bit too complex to serve well as illustrations for those who are not already familliar with the lightpath.
I might actually start showing this to my students, the whole video is remarkably well made.
Thanks for the kind words! Really appreciate it, especially from someone that actually knows the subject matter and knows what they are talking about! I'm definitely an optics beginner so it's encouraging to hear there weren't too many mistakes made :)
Super ambitious project, wow! Very impressed you got any images. Would definitely want better / faster scanning system but it does work so that's amazing.
Congrats on making a convocal! I build microscopes for biological research in my phd for living. Some tips: it seems there are is lot of aberration in the spot at the pinhole, resulting in bad contrast. Use a mirror (in focus) and try tilting and moving the second lens to get a bettet spot. You probably want a kinematic mount for that lens to make the alignment easier.
This project sounds like a perfect candidate for a somewhat beefy microcontroller. Something like an STM32H series. Integrating the amplifier, stepper drivers, and laser driver onto a single board with an MCU would reduce the noise issues as well as latency.
This isn't that different from a 3D printer so one might even be able to use Marlin or Klipper firmware to run it. I don't know offhand if either of them would be able to output the intensity data in an easily digested format but I suspect they could.
Agreed! I really need to learn me some better EE skills so I could integrate this stuff a bit better than breadboarding :)
Cool project. One of the reasons confocal can be so good for biology is that it uses fluorescence, so you get isotopic emission from each point with little effect like absorption or reflection differences. Would be interesting to see if you could coat your samples in a fluorescent dye and add an emission filter if it would significantly improve the quality.
I find it absolutely amazing that you built this yourself WOW!! Thanks for sharing
Really interesting! Did you try to process the complete 3D volume in ImageJ (or Fiji) instead of generating the 2D image of Z-profile maxima?
I did! Unfortunately ended up cutting those from the video, due to some technical issues and because the video was running quite long. Here's the "E Pluribus" section of the penny, visualized in VolView: imgur.com/a/jwwH17y and here is an alternate version of z-maxima where it takes the top 50 points around each maxima: imgur.com/a/YXoShko. And here is the other section of the penny: imgur.com/a/MgIjihB
Definitely interesting to look at, and helped debug some issues but made seeing the surface harder.
I've worked with confocals, and the easiest way to get the pin hole and X/Y/Z stage is to use an optical fibre for the pinhole then move the fibre tip. Also we used photomultiplier tubes which give you much better sensitivity.
Ah, that's clever! I assume you have to use a single mode fiber, or would a larger multi-mode work? That would certainly cut down on the complexity of the optics and alignment!
You could also get a really quick profile using a camera in reflected brightfield. Image a focus series in Z, and then do an Extended Depth of Focus in FIJI (ImageJ). This will return a height map identical to the one you are getting with the confocal. Spiral scanning and photomultiplier tubes will also greatly increase your speed. Finally, a Teensy running in DMA mode can do dual channel ADC at 1.1 MHz per channel which can then be dumped from RAM to an SD card for rapid storage and later processing.
I wouldn't mind seeing you improving upon this. I was able to find a height map of the obverse of a Lincoln cent elsewhere online, and that was an amazing help in creating a model of the bust. If there were some way to get scans of any coin like that, it'd be absolutely amazing.
You may also consider a diode sensor array for faster imaging. I would imagine more optical points of interest pulsed at the correct intervals to avoid interference would significantly decrease the scanning time.
This would not work in the way you suggested. The array would sample your Airy spot and not the sample space. Instead this idea is used today to generate super resolution.
We're still under 100 comments and I'm subscribed to a chunk of the commenters that left them lol. I feel like I'm with my people here (not for long of course, remember us when you get that gold button!)
Amazing job with the intro by the way. Probably obvious but still needs said. Guess I can unpause and watch the rest now haha.
first thing that comes to mind is reflectivity would greatly affect the results and create ALLOT of noise.. because after all, your relying on the reflection of the laser to plot the data.. so if the surface of what your measuring has a higher reflection than that of other points, then it will throw it off, because your measuring the reflection at a specific Z point, as opposed to the actual surface height. this is why electron microscopes work so well, because an electron cares less about reflectivity of light upon the surface that its measuring.
Omg you are so smart, and I am so in love with this project!
at college they talked about improving scanning electron microscopes by using a DLP mirror array to be able to scan so much faster. May be worth investigating if you're interested, but I have no idea the technical challenges that this would require to overcome.
Amazing work. I think there's a lot more you could do on the optimization side - like setting the z scan range based on the height of adjacent points (although if you're post-processessing the data, you'd have switch to doing some of that in real[-ish] time). I think this would particularly help in things like the screw threads (unless you're physically limited in range by something else).
Would it be possible to trade off precision for sample volume? (sounds like it would at least require re-gearing the stage motors)
i have learned more about building optical set-ups from this video than in all of my 3 years in an electro-optics phd program
coming from the field of microcopy im impressed at what you were able to make on the basis of these rather simple devices! keep going!
did you actualy try imaging a clean, flat surface? It seems arbitrary but you might get information about your noise (and if you try different materials, there might even be different noise values due to different reflectances of these materials).
Yunno, I didnt... but that's a great idea. Could probably use that to help calibrate/clean up the images too.
I would suggest trying something call white light confocal instead of intensity only pinhole confocal, but you need a spectrometer which can also be quite easily made as theres little need for narrow FWHM, a commercial version will be chrocodile from precitec, it gives depth info and you only need to scan in XY, plus with different chromatic abberation lens, you can get different scan range, something like 100um to few mm dynamic range
Hehe, on the todo list actually! I discovered the Nanovea version of the same thing (I think they call it "chromatic confocal" instead, just to be confusing i guess) while working on this project, but was too invested in the regular confocal to quit at that point. I agree, it looks great! Should be so much faster, and it's such a clever mechanism using/abusing chromatic aberration. I think the optics should be pretty straightforward, right? Just a bunch of regular lenses stacked up to increase the chromatic aberration at each lens?
@@BreakingTaps yes, the optics are very straight forward, calibration is a bit tricky, but doable in a home shop i think, we bodged together a chrocodile taped to a benchtop cnc router and did some mapping that way, it worked alright as at high speed weight will average out imperfections, didnt even need filtering. one thing chrocodile can do is 4KHz readout, with a tiny DSP, i will think with a FPGA demo board it will be equally good.
20:57 Hilarious to me, that I know nothing about microscopy or any kind of precision metrology, but when you were talking about the images you took, and the issues they had, I came up with this exact same solution.
This is why I love youtube. Fantastic work.
I bought a used Keyence LT-9500 it uses piezo actuators to move the laser it is an amazing piece of tech available on the used market.
My guess is that for some images the normal of the surface matters very much (e.g. the screw). Thus you don't get the light back as it's reflected in a different direction
Yeah I think you're probably right, between being highly reflective and also at a very bad angle, probably very little light probably made it to the sensor.
What a great video! I would be interested to see if you could improve on the amount of time it takes to scan by implementing a gradient ascent technique to try to move the stage closer to the focal point without scanning the entire range. You could also use the surrounding pixels to try to determine a good Z starting point for the gradient ascent at the current pixel. Not sure what kind of effect this would have on processing time though.
Holy cow. Hidden gem of a channel. Proud to say I was here before he hits 10 million subs!
I was reeeeaaaally hoping/expecting to see it in operation. Literally laughed out loud when I saw that op-amp circuit. I have no idea how it works (I'm a digital/battery/power guy... poor excuse), but just how you were like "lol I pooped this out" was amazing. Still, you got a sub out of me. Good stuff!
You may be able to build a small piezo stack for ultrafine travel. Combined with linear encoders, you'd have the ability to move within your typical tolerance to sub-micron. (i.e. stepper moves to position, encoder receives a call to provide the precise position value, and a differential voltage is applied across the piezo stack to provide movement offset) The traditional large assemblies wouldn't be needed for this sort of payload, might be able to DIY something up with a few piezo crystal stacks.
Edit: Just checked a local supplier, they're $77 for a stroke length of 17.4 microns, dynamic load force 200N rated.
I used to use a KLA Tencor Confocal Review Station when I worked for a certain large semiconductor company. Normally we just used the optical microscope. I thought it was a really neat tool but we couldn't save pictures from it to our database. The only way we could save them is to print them which was expensive and slow.
I absolutely love thoughts scientific video! 😀😀😀
Would like to see more of them. I know there are a lot of work but the result is soooo fucking amazing!
You do some awesome projects! This was very cool!
I had a similar issue with scan time on an IR camera I built, based on a single-point IR detector and a couple of silicon mirrors, also driven by stepper motors. In the end, I got it to a) scan the scene at very low resolution and then b) automatically pick points of interest (essentially, hot bits) and go back and scan around them at higher res.
Wouaw, many thanks the video! This is an amazing work!
Two thoughts: 1. How about using a nozzle as a pinhole. 0.1mm nozzles are pretty cheap, and you could always drill out the back if you need more room for the beam to expand. They come with a convenient screw thread for mounting and fine adjustment along the beam path! 2. RobRenz has a video on an autocollimator mirror system with some interesting differential screws for the precise positioning of mirrors. Been trying to figure out if it is possible to make a 3D printed laser autocollimator...
Dude the cinematography in this is NUTS
I love every single piece of this. Instant sub