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Shack-Hartmann sensor resolution - how much is good?

If you are new to adaptive optics (AO) like me, the selection of right hardware can be daunting. Starting with a wavefront sensor - they range in price, resolution, and many options which are not obvious. By practical trial and error I learned something about resolution, which wasn't obvious to me a year ago.

The Shack-Hartmann wavefront sensor (WFS) is essentially a camera with a lenslet array instead of an objective.
 There are sensors with 15x15 lenses, 30x30 and higher. Naively, you might think "the more the better" - we are digital age kids used to get high-res for cheap.

However, there is a catch. High-res sensor, say, 30x30 lenslets, divides your photon count by 900 per spot. Roughly speaking, when you image a fluorescent bead (or another point source) by a camera with "normal lens" (not a lenslet array), and your peak intensity is 2000, this makes a very nice, high SNR bead image. However, is you switch to Fourier (pupil) plane and image the wavefront u…
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Control of sCMOS cameras with Python

Running a sCMOS camera using a software with GUI is nice, but at some point I want to control the camera from Jupyter notebook, so that I can acquire images and analyse them on the same page of code. Unfortunately many camera manufacturers don't provide Python API (any of them do?). So the hard way would to ferret out camera's drivers (.dll files), figure out the names and arguments of functions, and write a home-made Python wrapper for a DLL file using ctypes, like I did for Thorlabs wavefront sensor. This is a way of tears and pain.

Luckily, there is a silk road to the camera control. The API for many cameras and other instruments is already implemented in MicroManager, which also has a Python wrapper MMCorePy  around it! So, after quick and easy installation of the MMCorePy, Python code becomes simple and clean, with all heavy lifting done in MicroManager API running under the hood:


Programming NI DAQmx board in Python: easier than you think!

For my DIY microscope I had a task - generate a train of digital pulses which simulate camera trigger, so that other devices (galvo and laser) are synched. I wanted to do it in Python, so that it seamlessly integrates in my data acquisition and analysis Jupyter notebook.

After some quick search I found a PyDAQmx library which seemed mature and had good examples to begin with.

Installation was smooth: download, unzip, open Anaconda prompt,
python setup.py install

After only 30 min fiddling, I was able to solve my problem in just a few lines of code:

Holy crap, it just works, out of the box. Oscilloscope shows nice digital pulses every 100 ms, each 1 ms long. The code is much shorter and cleaner than would be in C, C#, or LabView.

PyDAQmx appears to be a full-power wrapper around native NI DAQmx drivers (yes, they need to be installed), so presumably it can do all that can be done in C or even LabView (this statement needs to be tested).

One can use PyDAQmx to control galvos with fast ana…

Programming of DIY microscopes: MicroManager vs LabVIEW

In the flourishing field of DIY light microscopy, a decision of choosing the programming language to control the microscope is critically important. Modern microscopes are becoming increasingly intelligent. They orchestrate multiple devices (lasers, cameras, shutters, pockel cells) with ever increasing temporal precision, collect data semi-automatically following user-defined scenarios, adjust focus and illumination to follow the motion (or development) of a living organism.
So, the programming language must seamlessly communicate with hardware, allow devices be easily added or removed, have rich libraries for device drivers and image processing, and allow coding of good-looking and smooth GUIs for end users. This is a long list of requirements! So, what are the  options for DIY microscope programming?

There are currently two large schools of microscope programming - Labviewers and Micromanagers. (update: Matlab for microscope control also has a strong community, comparable to labview…

3D modeling in a lab

About once a week I am asked by my colleagues which 3D modeling software I am using - usually when I am staring at the new part being 3D printed.

I am using Autodesk Inventor for a few reasons:
it is a professional software for engineers and has huge community around itit provides freeacademic licensethere are thousands of youtube videos with detailed tutorials by enthusiastseasy to learn at a basic level, but there is always a lot of room for growth In a lab, there are two main workflows where Inventor is necessary: 3D modeling of complex assemblies (like custom-built microscope) and 3D printing. There are many youtube tutorials for beginners, so I here only review some things that Inventor can do, without any specific instructions.  3D modeling of parts and assemblies Before building a new microscope, you can create its virtual model and check dimensions, required adapters, and whether things will fit together. Luckily, Thorlabs has 3D model of nearly all its parts available for fre…

How to connect a rotary encoder to Arduino, make your own PCB board, and be happy

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. The yellow and…

Machine shopping for a microscopy lab

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 or small as you m…