Kyle M. Douglass
@kmdouglass.bsky.social
Researcher in Optics and Biophysics @ EPFL | Computational, Label-Free, and Fluorescence Imaging Specialist | Software Engineer https://kylemdouglass.com
I've been playing with PyTorch's autograd for only one week and already I lay awake at night wondering whether my latent variables are flowing differentiably through my inference chains. #everydayproblems
#Radiometry is a challenging topic in #optics because the physics and the mathematics are often presented together as one subject, when in reality there is a clear delineation between the two. Here I provide a primer on the basic mathematics of radiometry. kylemdouglass.com/posts/a-prim...
I added beam scanning capabilities to our lab's vector focal field simulation library just now: github.com/LEB-EPFL/jus... You can use it to simulate beam scanning using arbitrary vector beams in the focus of a high NA microscope objective.
GitHub - LEB-EPFL/just-focus: Vector electromagnetic field calculations in the focus of high NA microscope objectives.
Vector electromagnetic field calculations in the focus of high NA microscope objectives. - LEB-EPFL/just-focus
github.com
I started a thread on Microforum searching for cameras similar to the Photometrics Kinetix and have shared a spreadsheet with my search results. If you know of others that fall within this category, then please do share. forum.microlist.org/t/equivalent...
Equivalent cameras to the Photometrics Kinetix?
Thanks again @Hazen_Babcock . It’s a good point to look at the sensor itself. Here is the spreadsheet I compiled of similar cameras: Proton Drive The cameras I looked at were: Photometrics Kinetix...
forum.microlist.org
Last night I learned that the effective focal length of a lens can differ in the backward and forward directions if the refractive index of the media in object and image spaces differ. I think often about how little we treat this scenario in #optics education given its ubiquity in #microscopy.
Is the infinity mark on cheap machine vision lenses always this wrong? This is the setting at which I'm able to focus on some clouds 🤔 Am I missing something? #optics #computervision
Do you write/want to write drivers to communicate with (scientific) instruments in Rust? Check out my latest blog post on how to make this hopefully easier in the future. Comments, ideas, etc. are always welcome. blog.galactic-forensics.space/blog/07-inst... #Rust
instrumentRs v0.2.0 design ideas
Thoughts and ideas...
blog.galactic-forensics.space
You can place a mirror at 45 deg. AOI at the focus of a lens whose back focal distance is known by using a ruler with straight edge against the lens housing and extending beyond the mirror. Under collimated input, the intersection of the reflected beam with the ruler should be the BFD. #optics
"What we saw was this pretty striking pattern that software engineers got about 20% more feedback if they were sitting near their colleagues than if they were distant from them... It was [young workers] who had the most to learn that really saw this deficit in feedback." www.npr.org/2026/06/01/n...
Remote work -- not AI -- has sidelined recent college graduates, research finds
Research from the New York Fed finds that younger college graduates have been sidelined by remote work in recent years, as companies may be reluctant to hire those needing more training and mentoring.
npr.org
Using a wavefront sensor and bisection to place the focal plane of a microscope tube lens in the back focal plane of an objective lens. I used beam diameter as the readout because the radius of curvature did not change significantly over the range of lens positions that I tested. #microscopy
I'm still trying to work out whether this is truly useful, but you can use a coverslip to pick off the beam from an alignment laser that is back reflected from a mirror at the end of a setup (not shown). Deviations of the beam upon insertion of a lens indicate its misalignment. #optics
I added a galvo and scan lens example to my Cherry ray tracer to help one of our PhD students understand scan systems. Click and drag on the theta rotational offset value for the first mirror surface to see what happens to the ray fan in real time. #optics #microscopy kmdouglass.github.io/cherry
After 9 years, I am finally finishing the story about normalized cross-correlation (and reviving my blog). The new blog post about deep technical details on the most used image registration technique. I know y'all have been waiting. katpyxa.info/feedbacks/?p...
Calculating normalized cross-correlation (part 3) – //><=~!=//
katpyxa.info
"[I]n any science less complete than physics, the more general mind still has its uses, though everyday the chances grow less." C. P. Snow, lamenting the loss of synthesis within a science as it matures.
When a single line of code you wrote without thought three years ago leads to three weeks of nightly debugging after the kid goes down. Ray-Surface Intersections with the Newton-Raphson Algorithm kylemdouglass.com/posts/ray-su...
Ray-Surface Intersections with the Newton-Raphson Algorithm
I take a deep dive into computing ray-surface intersections using the Newton-Raphson algorithm.
kylemdouglass.com
An apologia for theoretical biology. From "Energy Flow in Biology" by Harold J. Morowitz.
"Optimal lens design and use in laser-scanning microscopy" doi.org/10.1364/BOE.... #optics #journalclub
I implemented folds into the Cherry Ray Tracer today. Rather than freely placing components in space, I took inspiration from video games and used a RUF coordinate system to build up the system surface by surface. kmdouglass.github.io/cherry kylemdouglass.com/posts/3d-seq... #optics
Does anyone have any tips for putting a galvo in the center of a 4f system in the scan/descan arm of a laser point scanning fluorescence microscope? I normally align everything to the objective, but here I wonder whether the galvo should be the primary datum to align to.
I can never remember the electrostatic conventions for the mitochondrial membrane potential, so I wrote them down: kylemdouglass.com/posts/electr...
I finally managed to rewrite the Cherry Ray Tracer GUI using egui, an immediate mode GUI for Rust with WASM support. In addition, I figured out threading in WebAssembly via SharedArrayBuffers, so this thing is now lightning fast. kmdouglass.github.io/cherry #optics #wasm #raytracing
Last week I learned that I can use the internal counter on a NI-DAQ board as a triggerable pulse sequence that serves as the clock for an analog output waveform. Pretty cool! #microscopy kylemdouglass.com/posts/trigge...
Triggering Analog Voltage Outputs using a NI-DAQ Counter
I explore routing signals from counters on a NI-DAQ device for custom triggering and waveform generation.
kylemdouglass.com
I finally got around to writing the discussion section of our lab's basic training course on live cell #microscopy. I explain the tradeoffs involved in designing an imaging experiment and the art of thinking of the experiment as an optimization problem. leb-epfl.github.io/basic_traini...
Introduction - Microscopy Basic Training
leb-epfl.github.io
I had the happy realization the other day that conservation of radiance / étendue is purely geometrical. Radiance is just proportional to the size of the set of all lines through two area elements, and the product of area and solid angle is an invariant over this set. #optics #radiometry
A holiday demonstration of the different penetration depths of red and blue light into tissue. #optics
When X-rays are incident upon a crystal, some of their energy is reflected from the lattice planes. Certain angles of incidence will lead to the observation of diffraction peaks due to constructive interference between the reflected wavefronts. #optics #microscopy youtu.be/FZ4gilAe7x0
The Bragg Condition
YouTube video by Kyle Douglass
youtu.be
The construction of the support of the 3D aperture (a.k.a. the optical transfer function or OTF) using the Ewald sphere in a brightfield microscope under partially coherent illumination. #optics #microscopy
How to use the Ewald Sphere to determine the support of the 3D aperture of a brightfield microscope under coherent illumination. #optics #microscopy
Object models for image formation theory in brightfield microscopes. kylemdouglass.com/posts/image-...
Image Formation in Brightfield Microscopy: Part 1 - Object Models
I describe how objects are treated in image formation models for brightfield microscopy.
kylemdouglass.com