This blog post serves as a link to a case report about the debugging of a two-photon microscope which showed a too low fluorescence yield. With the help of the internet, I singled down the cause of the problem to the dispersion of the femtosecond pulses by dielectric mirrors in the microscope. The lessons learned from that have been summarized before on Labrigger’s blog (also check out the comments!).

However, I think it makes sense to report this debugging attempt in a bit more detail, and probably there are two-photon microscope users who are keen on understanding more about the technical details and could profit from such a technical report. It includes not only nice pictures, but also several useful lessons that can be learned from that, some obvious or well-known, others not so much.

I used this occasion to try out a Github-based publication template provided by Andrew York. This template is written in a publication-like style, but in HTML, which allows to take advantage of some degree of interactivity and the embedding of web-links. The advantages compared to purely pdf-based publications are obvious; platforms like distill.pub show, although limited to the field of machine learning, how the future of publishing could look like: interactive, open, possibly based on web interfaces instead of a focus on print.

For me, using this template was an attempt to familiarize myself with this sort of publishing, and to test how difficult is to use such a template. I hope you enjoy the read:

Pulse dispersion, dielectric mirrors and fluorescence yield: A case report of a two-photon microscope.