So Long and Thanks For All the Fish

I start work at Zymergen tomorrow morning; UCSF had a nice send-off for me on Friday. My UCSF email doesn’t work anymore but I can still update this blog. There probably won’t be many more posts here; I intend to focus on my new job and I don’t think anyone at UCSF plans to post here. I do think that it will remain up for a while, but there are no guarantees of that.

This site is licensed under a Creative Commons-Attribution-Share Alike license, meaning that anyone can create a copy of it, provided that they attribute it to me and license their copy under similar rules. So if you want to make copies of part of the site, feel free to do so. If you want the whole thing, let me know and I can send you a wordpress dump. is also licensed under very permissive rules, so you are also welcome to make copies of that (although that should not go anywhere – it’s hosted on github and I own the domain name). I’m also happy to re-license the content of either site if there is a good reason to – just let me know.

With regards to, I’d like to keep that up to date, and am willing to put in some effort to do so. If you have changes to suggest, the best way to do so is to submit pull requests to the github source, but you are also welcome to send me (p)reprints of papers describing new fluorescent proteins and I will add them to the website.

I do hope to put up one or two more posts – I have a few more things to say about the AZ100 light sheet scope we built and I have some thoughts on the evolution of core facilities over the last decade I’d like to write up, but no promises.

Finally, keep in touch – I’m on twitter as @ScopeKurt, and you can email me at kurt dot thorn at gmail dot com.


Position available at the NIC@UCSF

The Nikon Imaging Center at the University of California, San Francisco seeks an imaging specialist to work with the director of the center in maintaining the day to day operations of the center. The Nikon Imaging Center at UCSF (NIC@UCSF) is a partnership between Nikon Instruments, UCSF, and a number of other vendors that provides eight state-of-the-art microscopes for use by the UCSF community. These microscopes are used by approximately 300 scientists a year and contribute data to approximately 40 publications a year. To learn more, see our website.

The successful candidate will be the initial point of contact for users seeking to use the NIC and will be responsible for advising them on the choice of microscope for their experiment and will provide training on the microscopes. The candidate should be sufficiently knowledgeable about microscopy and biology to advise newcomers to microscopy about the appropriate microscopes to use, given their experimental requirements and constraints. This individual will also be responsible for routine cleaning and maintenance of microscopes, testing of microscope performance, and troubleshooting problems with the microscopes. Within these parameters, the successfulcandidate will have considerable freedom which could include collaborations with NIC users.

A PhD degree in biology, physics, optics, or a related field is required as is previous experience with light microscopy. Previous experience with equipment maintenance and training in a core facility environment is desirable. We are particularly looking for candidates with experience in biophysics, programming, or development of microscopy hardware.

UC San Francisco seeks candidates whose experience, teaching, research, or community service that has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status.

The official posting is not up yet, but when it is it will be available at

In the meantime, if you’re interested in the position please send your CV and a cover letter to DeLaine Larsen,

Why I’m leaving UCSF; or thoughts on running an imaging center for those who might consider it

After a little over ten years running the Nikon Imaging Center at UCSF, I’ve decided to take a job in industry. On March 6th, I will start work at Zymergen. DeLaine Larsen will take over as director of the NIC. At Zymergen, I won’t be doing much, if any, microscopy. Instead, I’ll be learning a lot and working to help them with their strain optimization efforts. It’s bittersweet to be leaving – I’ve really enjoyed my time at UCSF and I love microscopy, but it’s time to move on and to try something new. Here, I want to say a few words about why I’ve decided to leave UCSF, with the goal of hopefully shedding some light on the challenges of running a core facility that might be of interest to someone considering this career path. Continue reading

Nikon and UCSF parting ways; thoughts on managing core facility funding

Nikon has supported the Nikon Imaging Center at UCSF since its inception in 2006. During that time they have provided both direct financial support as well as providing six microscopes to the center, and then replacing and upgrading those microscopes in 2009/2010. Our relationship with Nikon is now coming to an end; we will retain the microscopes we have and Nikon will provide service on them for some time, but we will not get new hardware, nor we will get financial support after 2017.

(For those of you worried about the future of the NIC; we’ll be fine. Recharge rates will go up, but that will be the only change in the near term.)

Not surprisingly, given this change in affairs, I’ve been thinking a lot about our financial model and I wanted to share some of that thinking here in case it’s useful to someone else who is new at core management. Continue reading

Access problems with https://

I’ve had a couple of reports of people unable read the posts by clicking on the front page links. At least some of this is due to the blog only being set up to work with HTTP.  If  you try and access pages through HTTPS, you’ll run into problems. The way to fix this seems to be to switch all links over to HTTPS.  I’ll do that in the next few weeks (unfortunately, it’s not totally straightforward), but in the meantime, if you can’t access a page, try accessing it via http:// instead of https://.

A new year, a new blog post

Readers of this blog may have noticed that there has been a decline in the number of posts in the last year or two. Between home (a toddler) and work (an R01 grant) my life has gotten busier and I’ve had less time to make posts on this blog. I’ve decided that I should reverse that trend. A number of people have told me that they’ve found one post or another useful, and so despite the small number of pageviews (about 100 a day), it seems like this site is providing a useful service.  It also seems like a good way to promote myself and make people aware of what I do in a field (core director) that doesn’t lead to a lot of publications.

Finally, I enjoy posting here and sharing some of the details of projects we’re working on. My goal is to produce a least one substantive post a month, in addition to the paper roundup and occasional brief notification of something interesting. Two major projects in the NIC right now are development of a simple light sheet microscope, and commissioning of a  CSU-W1 spinning disk confocal integrated with our high-speed widefield microscope. Both of these have a number of interesting technical challenges that may be of interest to the larger microscopy community, and I look forward to sharing them with you.

Feel free to hold me to the one interesting post a month, and complain if you don’t see it. 🙂

Server update

A couple of people have contacted me with problems posting.  I just replaced our old self-signed certificate with an official SSL certificate, so I’m hoping that fixes these problems. If you’ve had problems commenting previously, can you try making a comment on the post and email me with the error message if it fails?