Preprint: Review of Genetically Encoded Fluorescent Tags

I was recently asked to write a brief Technical Perspective on fluorescent tags for Molecular Biology of the Cell. These are meant to be introductions to a topic for novices in the field; I previously wrote one on light microscopy.

I’ve posted a preprint of the fluorescent tag review here; please send me any comments and I will incorporate them into the final version. I would have posted the preprint on BioRxiv, but it seems that they don’t host reviews.

XKCD on étendue

Today’s xkcd what if is about one of my favorite topics, étendue.  I discussed it briefly a little while ago, but briefly it says that the area of a light source times its solid angle as seen by the optical system must be a constant when propagated through that optical system. It’s a topic that can be counter-intuitive and takes some time to understand, and the XKCD explanation is actually quite good and relatively easy to follow – I would definitely recommend it as an introduction to the topic.

A quick guide to light microscopy in cell biology

A few months ago, I was asked to write a introduction for newcomers to light microsopy for Molecular Biology of the Cell (MBOC). That paper is now out, and I’m pretty pleased with how it came out. It’s designed to provide a brief introduction to a graduate student or postdoc in cell biology who’s new to microscopy and wants a brief orientation to the field.

I’ve taken to turning down offers to write reviews because in general, I don’t think the impact is worth the effort required to write them (I also don’t like signing my copyright over to the publisher). I agreed to write this one because I think MBOC is a good journal – they focus on good science and all papers are freely accessible two months after publication and the Technical Perspective fills a useful role of providing orientation to newcomers in a field. I actually had a lot of fun writing the paper – it was nice to be able to sit down and write without having constantly refer to the literature or to data.

Online Microscopy Courses

I haven’t been posting much here lately – I’ve been busy with getting my lab up and running and busy with a number of other responsibilities at work. One of the many things I’m doing is putting together a graduate course on microscopy for students at UCSF, which led me to look at what online microscopy and optics courses are out there.  There’s a couple nice ones, which I’ve compiled on the NIC wiki.  If you know of others, please let me know in the comments.

Building a diSPIM

Hari Shroff and Abhishek Kumar have a fun post and video up describing building a diSPIM system at the Bangalore Microscopy Course. The video in particular is entertaining – it’s a time lapse showing the system assembly from start to finish. The 2015 course is now being organized – the web page isn’t up yet, but I encourage you to keep an eye out for it if you’re looking for a microscopy course to attend – the faculty are very good and the course is terrific (and a lot of fun!)

Book Chapter on Digital Microscopy

Nico Stuurman and I have written a chapter on digital microscopy for the forthcoming Handbook of Digital Imaging from Wiley.  Thanks to the UC open access policy, you can read the manuscript of the chapter for free.  The chapter provides an overview of biological light microscopy with specific details on camera choice and computer control of microscope hardware for automated acquisition and high speed hardware synchronization.  You can access the manuscript here.

The 2014 QB3-UCSF Course in Biological Light Microscopy

Just a reminder that I am once again co-directing the QB3-UCSF Course in Biological Light Microscopy and we are still looking for students to attend the course.  Here are the details:

August 3 – 9, 2014

Genentech Hall, UCSF Mission Bay

Directors: Bo Huang and Kurt Thorn

This course provides an intensive introduction to the theory and practice of light microscopy, beginning with optics and continuing to the latest super-resolution techniques.

The course includes didactic lectures from a number of UCSF faculty in their areas of expertise and hands-on laboratory sessions with state-of-the-art microscopes. Specific topics include: basic optics (build your own optical rail microscope); fourier optics; brightfield contrasting; fluorescence microscopy and probes; confocal microscopy; TIRF; two-photon, FRAP/FLIP/photoconversion; and super-resolution microscopy

Laboratory work and lectures will be held at the UCSF Mission Bay campus. Course tuition is $2,295, including lunch and dinner. Stipends for tuition are available.

Attendance limited to 24 students. Please apply by April 15, 2014.

For more information and to apply see the course webpage or contact me directly.

Sponsors include QB3, Nikon, Technical Instruments, Agilent, Photometrics, and Andor; full list here.

Please forward to anyone who may be interested.