Instrument Control for Microscopes and Accessories
ScanImageB is a software developed by myself for the control of a two-photon resonant scanning microscope. The adapters for stage controller and pockels cell as well as the look and feel of the GUI are taken from Scanimage 4.2, a freely accessible software developed in the group of Karel Svoboda in Janelia and continued semi-commercially.
Under the hood, I changed the main processing lines, mostly inspired by scanbox.wordpress.com (Dario Ringach). I'm using a Alazar 9440 DAQ board for laser-pulse timed acquisition at 80 MHz and NI 6321 DAQ boards for synchronization and instrument control. The reason for uploading this software is 1) version control for the lab I'm working in and 2) offering the possibility to point other researchers/programmers to interesting parts of the code. The software as a whole is NOT supposed to be self-explanatory, and it is not intended to be. (There is no comparably complex microscope control software that is self-explanatory, and all of them require costumer support by one or more persons, which I cannot provide.)
This software has been used for two-photon calcium imaging for example in the following papers: paper 1, paper 2, paper 3.
Some interesting lines of code are pointed out in this blog post.
The Voice Coil Control Loop is a small control script used for positional control of a voice coil motor for fast z-scanning as described in a research paper published in Biomedical Optics Express: https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-5-1656 .
The Reglo ICC Matlab Class is a Matlab adapter to control a 4-wheel digitally controlled peristaltic pump (http://www.ismatec.com/int_e/pumps/t_reglo/reglo.htm). The company provides a control software and a Labview control VI, but no Matlab control interface. I used the serial commands provided by the pump manual to write this adapter.