Job Posting: Director of the Gladstone Histology and Light Microscopy Core

First, apologies for the infrequent posting of late. Due to both literal and figurative (a new R01) children, I haven’t had much spare time to post here. I hope this changes in the future.

Second, I’m helping the Gladstone Institutes, across the street from UCSF, recruit a new director for their microscopy and histology core.  The full job ad is below, but briefly, we are looking for a PhD to direct the day to day operations of the core, which would include microscopy training, maintenance, advising users on how best to acquire the data they need, and overseeing the histology operations.

This position has the potential for a lot of freedom and growth; the ideal candidate will play a major role in shaping the imaging resources available at the Gladstone Institutes and UCSF.

For more information and to apply, see the following link:
https://careers-gladstoneinstitutes.icims.com/jobs/1099/staff-research-scientist/job

Postdoctoral positions in my lab

I recently got an R01 funded and so I am looking to hire two postdoctoral fellows to work on a project to develop novel bead-based biochemical assays. This project seeks to apply our recently developed technology for making spectrally encoded microspheres (see Gerver et al. Lab Chip 2012) as a substrate for developing novel assays for probing antibody reactivity in patient samples.
One postdoctoral fellow will head the assay development part of the project, and must have substantial experience in biology and or chemistry. Experience with peptide synthesis or antibody binding assays is a plus. The second postdoc will develop new microfluidic devices to automate these assays and must have substantial expertise in microfluidic device design and fabrication. For both positions, programming experience is desirable. Applicants must have a PhD or expect to receive their PhD by the end of the year.
This project is a close collaboration with Dr. Joseph DeRisi at UCSF and Dr. Polly Fordyce at Stanford University, and the individuals hired for these positions will work closely with both of these laboratories. In particular, the postdoc working on the microfluidic aspects of this project will be expect to spend part of his or her time at Stanford in the Fordyce lab.
To apply, please send your CV and names of three references to me: kurt.thorn@ucsf.edu.

A movie about Klaus Kemp, diatom slide maker

We have long used diatom slides as nice test samples and resolution targets for brightfield microscopy. The diatoms have silica shells with regularly spaced small holes in them. The hole spacing varies from species to species and ranges from a few hundred nanometers to a little over a micron, making them perfect for showing the affect of NA on microscope resolution. For a long time, we have gotten slides from Klaus Kemp, who is apparently the last producer of diatom slides.

The New York Times is now hosting a very nice short movie on Klaus’s work, called The Diatomist. It’s worth checking out if you’ve ever used a diatom slide or wondered what went into making them.

What journals should I (do I) read?

In order to keep up with the literature, I use a two main strategies. I use Readcube for reading PDFs on my PC. Readcube includes a recommendation engine which is surprisingly good.  I’m not sure how it works, but I imagine it uses text similarity or co-citation to find papers like the ones in your library, and it’s found a number of interesting papers for me that I otherwise would have missed.

I also use the much more old-fashioned strategy of reading journal tables of contents. I have Feedly set up with the RSS feeds for a number of journals and scan it in my spare time to find interesting papers. These two strategies are where most of the papers in the monthly paper roundup come from.

Recently, I got interested in whether I was scanning the right tables of contents, so I decided to see what journals publish the most papers of interest to me. To do so I counted the number of papers from each journal that have appeared in the paper roundup section of this blog (about 200 papers total) and that appear in my Readcube library (about 600 papers total). I then normalized to the average number of papers each journal published over the last three years (found here). This gives a metric that is roughly how often that journal will publish a paper of interest to me (although I am comparing different time frames, so it’s not completely accurate).

Not surprisingly, Nature Methods tops the list, and Journal of Microscopy is number 3. Nature Protocols is number 2, although it often publishes groups of protocols on a theme, and I’ve cited all of them in the past, potentially boosting its ranking. More surprising to me is that the list contains a bunch of neuroscience and chemistry journals.

I’ve updated the journals I follow in Feedly to reflect those that I most often reference. I hope that this list is of interest to you as well.

JournalRank (Blog)Rank (Readcube)
Nature Methods12
Nature Protocols219
Journal of Microscopy31
ACS Chemical Biology46
Current Protocols in Cytometry53
Cold Spring Harbor Protocols623
Nature Photonics711
Chemistry & Biology814
Chemical Society Reviews97
Current Opinion in Chemical Biology104
Cytometry Part A115
Biophysical Journal1215
Biomedical Optics Express1322
Nature Nanotechnology1425
Current Opinion in Neurobiology1517
Lab on a Chip168
Cell1724
Microscopy Research and Technique1820
Journal of Cell Biology1921
Nature Communications2048

ASCB roundup

I just got back from attending the 2013 ASCB meeting. I try to go every year as most of the microscopy vendors are there, so it’s a great place to see new products and network. I mostly didn’t go to the scientific talks, though there was one great talk by Eric Betzig on his latest developments on Bessel beam light sheet microscopy. He now has systems that can record a full volume in under a second and can image at high frame rates for hours with minimal phototoxicity. His results so outshone what you can do with commercial microscopes that I and several other microscopists found it thoroughly depressing.

On the vendor floor, there wasn’t any single new amazing product, but there were some nice developments.  There was also a lot of consolidation evident in the microscopy world: Andor, which recently purchased Spectral Applied Research and Apogee Imaging Systems, is itself being acquired by Oxford Instruments, and Prairie Technologies has been acquired by Bruker.  Here are some of the interesting things I saw:

  • Epi Technology – a startup making a reversed filter cube allowing you to image your epi-illumination source through the eyepieces. Useful for finding and removing dirt.
  • Datacolor is releasing a system for color calibration of transmitted light images. It uses a slide with known reference colors on it to allow putting your transmitted light images into a known color space using their own software. Unfortunately it doesn’t seem to plug in to any existing microscopy software.
  • Life Technologies has released a new DMEM formulation that reduces media fluorescence by about 9-fold.  It should be very nice for live cell imaging.
  • There were a number of companies showing off microfluidic systems for cell culture and imaging. Ebers, microfluidic ChipShop, and SynVivo were three that I talked to.
  • Nikon was showing off their new range of laser accessories, including a Mosaic-type micro-mirror system for patterned illumination, dual-arm TIRF, and a galvo scanning system for photobleaching.
  • Spectral Applied Research, recently acquired by Andor, which in turn is being acquired by Oxford Instruments, was showing off its all-in-one spinning disk, TIRF, and STORM system. It was quite nice looking but I can’t find any information about it on their website.
  • Bruker was showing off the swept-field confocal, formerly from Prairie technology. They now have it working for spectral detection, acquiring 16 wavelengths simultaneously at each point.

Statistics Resources

I recently came across a great website devoted to how statistics is misused in scientific reasoning (and how to use it correctly): Statistics Done Wrong. It’s a great addition to my other favorite statistics resource on the web, this guide to statistics [PDF] from an MIT intersession course.  While statistics isn’t exactly microscopy, it’s still important to know the right tools to use to analyze your data.