Light microscopy and adaptive optics, my uncensored and biased opinions

After I discovered the OpenStage project for cheap DIY microscopy stage automation, I decided to add a twist to it - control the stage positions manually with a rotary encoder, in addition to already-implemented serial port (USB). I found a nice RGB illuminated rotary encoder from Sparkfun  - it's shaft works as a button, and it is internally illuminated by built-in 3-color LEDs - a perfect device to switch speeds and manually control the stages. Hooking it up to Arduino seemed easy, and there is a very nice Encoder library to do just that. But when I started to test it, I fell into a deep rabbit hole called 'debouncing'. In short, real-world switches are never perfect and the 'moment' of switching has many messy things happening between the two leads, creating noise in the logic of reading device (Arduino). So, the voltage readout from a real rotary encoder looks like this: Note the high-frequency chirp in yellow line when it falls from high to low. T...

Disclaimer: I believe that everyone who can hang a picture on the wall can work in a machine shop. However, if you are sloppy, forgetful, or messy, don't do it. Or at least read the manuals and learn safety instructions before you go. If you are still reading this, you are not easily scared! Welcome to the world of DIY fun and creativity which a machine shop provides. Let's start with the most common myths. Myth 1. Machine shop is for old-school dudes who like to fix their motorcycles - today one can buy online everything needed for science. If you can buy everything - you follow mainstream, because your tools are old and popular enough that a company makes money making and selling them. If you hit an unbeaten path, or even make adjustments, you need to invent and make new tools. Of course, you can hire engineers - but research labs are rarely that rich. Myth 2. Machine shop is a big and expensive enterprise, only big institutes can afford it.  MS can be as big ...

Chemotaxis of bacteria is a molecular mechanism by which they sense chemicals and swim through  a biased random walk toward preferred concentrations. It has been studied extensively since late 60-s and became a triumph of quantitative system biology, thanks to giants like Julius Adler , Howard C. Berg , Daniel Koshland , to name a few. Perhaps the most instrumental in this scientific revolution was Howard Berg’s tracking microscope ( Berg 1971; PDF ), which could follow a freely swimming E.coli cell in 3D in real time . Yes, in 1971. It allowed precise quantification of cell swimming trajectories in spatial and temporal gradients of chemicals, which led to discovery that E.coli performs a biased random walk, with longer runs toward increasing concentrations of attractive chemicals ( Berg and Brown, 1972; PDF ). This work laid the foundation of quantitative approach to bacterial chemotaxis, which led to multiple breakthroughs on it’s biochemical and physical mechanisms. Even to...

Shack-Hartmann wavefront sensor is a brainchild of Cold War, born in late 1960-s by the need of US Air Force "to improve the images of satellites taken from earth"  -guess who's satellites caused such intense interest of Uncle Sam. The working principle is simple and elegant - the wavefront sampled by an array of micro-lenses, and its local slope is converted into displacements of focal spots: To make an SH sensor today, one needs an array of microlenses and a digital camera. The main difficulty is accurate calibration and the software which will convert camera images into wavefront reading. Thorlabs sells reasonably priced SH sensors and I purchased the WFS-150-7AR for my project. The good It is well built, comes with plate adapter and a C-mount ring adapter. The software runs smoothly and produces expected results (flat wavefront) when tested on spatially filtered and collimated HeNe laser. The manual is very detailed, and API comes in C, C#, and LabVie...

Gaussian beams    is a beautiful phenomenon in optics. As they propagate through space they retain their Gaussian shape, and only get broader or narrower. They are symmetric along the optical axis. No matter how many lenses you use to focus and defocus your laser beam, it will remain Gaussian. And it's shape is described by a few simple formulas , which define their thinnest section (w 0 , 'waist'), radius of wavefront (R), and divergence angle (Theta). Some immediate applications include fiber coupling, confocal microscopy, and light-sheet microscopy. The formulas describing Gaussian beams were derived in the 1960-s, soon after the invention of lasers, by solving the wave equation for electromagnetic waves, and were analysed exhaustively in paraxial approximation (Kogelnik and Li, 1966). Paraxial approximation means that angle of beam divergence angle is small (theta ~ tan(theta)). However, modern microscopy pushes limits to high-NA objectives and laser beam...

Mirao52e  from Imagine Optic is probably one of the best known high-stroke deformable mirrors (DMs), a working horse in adaptive optics. It has 52 actuators , huge stroke (up to +/- 50 microns peak-to-value), and a hefty 15-mm clear aperture of usable mirror surface. All things look good, at a price tag of about 20K euro . After some hesitation and comparing specs/price with Alpao mirrors, I eventually chose Mirao52e for my adaptive optics project. It is too early to speak of performance, I will do optical tests later. Today I can only share my first impressions. Pros: Small form factor: 64x64x17.6 mm, easy to integrate if your space is tight Very easy installation (Windows 7), basically installation of USB-serial port drivers  Cons: Mounting options are weird. There are two M3 tapped holes on each side, 20 mm apart. Does not fit any Thorlabs mount I know - they normally use M4 screws and 25-mm space between. No adapter included :( ...