Open, easy laser-scanning microscope software: LSMAQ
Years ago, Benjamin Judkewitz wanted to try some new techniques out with laser scanning two-photon microscopy. However, the software we were using was rather cumbersome to modify. So he wrote his own software from scratch (which took him roughly one day). The result was lsmaq.
LSMAQ is a lightweight and flexible laser scanning microscope acquisition software written in MATLAB. It supports National Instruments hardware for galvo-based scanning.
It does the essentials: it sends scan mirror commands out, reads image data in, and makes images. It has a live view and can stream to disk. He worked from that baseline to create the modified versions he wanted. It was a useful starting point for other people in the lab as well. Tiago Branco used it as a basis for two-photon uncaging software. I used it for arbitrary line scanning software in dendritic patch and imaging experiments. (Tiago, Ben, and I all overlapped in the Hausser Lab.)
It’s also useful for learning. There are relatively few lines of code, and the layout is straightforward.
Now, it is publicly available on GitHub, thanks to Ben.
https://github.com/danionella/lsmaq
This nice, I made something similar for TENSS (https://github.com/tenss/SimpleMScanner) but this LSMAQ is much more polished. You mention stage support in your README. Our 2p serial-section wrapper for ScanImage (https://github.com/BaselLaserMouse/BakingTray) has support for multiple stages in a non-hard-coded way. Maybe it will serve as the basis for what you want? The code for the stage control is here: https://github.com/BaselLaserMouse/BakingTray/tree/master/code/components/motion
Nice! Thanks, Rob.
Thank you Rob! I added a reference to SimpleMScanner, which I should have done much earlier. The stage is now slightly less hard-coded, but I will look at your code in more detail when the need for another stage adapter becomes more urgent (and will likely use it more than just as inspiration).
LSMAQ now supports pulse synchronization with low repetition rate lasers (tested with 1 MHz), as in three photon-microscopy.