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.

Position open on the Micro-Manager team

As readers of this blog know, I make extensive use of Micro-Manager to control our microscopes.  It happens that they are looking for a microscopist and programmer. Here’s the job announcement:

A Research Specialist position is open on the Micro-Manager development team. Micro-Manager ( is Open Source software for microscope control that is used in thousands of laboratories world-wide and has more than 50 code contributors. We are looking for a person with strong programming skills (C++, Java), who understands light microscopy (preferably has extensive experience with microscopes), can write documentation, and enjoys helping/teaching scientists work with microscopes. The Micro-Manager project is part of Ron Vale’s laboratory at UCSF and has about 2 more years of NIH funding. We plan to transition Micro-Manager to an independent (possibly non-profit) organization that will continue the core mission of Micro-Manager (to provide open source software tools for microscopists) but be financed more directly by those who benefit from its existence. The position requires a minimum of a Bachelor’s degree or equivalent (preferably in life sciences, physics, engineering or computer sciences) and demonstrable programming experience in Java and/or C++ as well as preferably one or more years experience with scientific imaging using light microscopes. In addition, the position requires excellent communication skills, great problem-solving abilities, and a detail oriented personality.

To Apply: Please submit cover letter, CV, and contact information for two professional references to

UCSF seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. UCSF is an Equal Opportunity/Affirmative Action Employer.

Laser cutting a dark box for an AZ100 microscope

Recently, we received a Nikon AZ100 on loan from a lab at UCSF that was no longer using it. We wanted to make it available for researchers to use, but we didn’t have a darkened space to put it in. Sitting on a lab bench, there was far too much stray light to be able to acquire fluorescence images. Since our sister lab, the Center for Advanced Technology, recently acquired a laser cutter, we set out to laser cut a dark enclosure for the microscope.


The final enclosure

Enclosure, close up

Close up

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As regular readers of this blog and the Micro-Manager mailing list will know, we’re big fans of the Arduino class of microcontroller boards for simple hardware control – controlling shutters and that sort of thing. For those of you who haven’t encountered them before, the Arduino is a microcontroller board with digital inputs and outputs brought out in a standard form factor and an easy-to-use programming language and development environment. I was inspired to make the post because I saw that Intel has now entered this space with the Galileo, a 32-bit, 400MHz Pentium system-on-a-chip that is Arduino pin compatible and runs both the Arduino environment and Linux.  It turns out that the digital outputs on this board are actually quite slow, so it’s probably not great for hardware control, but there is a really diverse set of Arduino compatible boards out there (Arduino | Wikipedia).  It’s not clear what the best hardware platform is for control of microscope hardware, but this is definitely an area I want to keep an eye on and hope to do more with in the future.