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:

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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 it it provides free academic license there are thousands of youtube videos with detailed tutorials by enthusiasts easy 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 it

How to connect a rotary encoder to Arduino and make your first PCB board

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

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 ga

Light microscopy and adaptive optics, my uncensored and biased opinions

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