Salk Institute for Biological Studies - Inaugural Director’s Blog Post

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Inaugural Director’s Blog Post

Inspired by Kurt Thorn, who no longer maintains his incredibly useful microscopy blog, I have longed for a forum to share exciting news about microscopy happening either here at Salk or anywhere else in the world. I will also use this space to make announcements on developments in the WABC, and will every now and then post sample data/images, advice specific to our instruments, or anything else that strikes my fancy. I will also occasionally allow for guest posts, when appropriate.

Most importantly, one of my favorite parts of Kurt’s blog was his “paper roundup”, highlighting papers that had interesting imaging or computational work relevant to imaging. The list below is most likely much longer than future lists, since this is my first post and I have a backlog of papers I’ve wanted to share. These should be of interest to the wider imaging community, but in particular people at Salk/UCSD/Scripps who use our facility:

High-density three-dimensional localization microscopy across large volumes (Betzig lab). Awesome work using lattice lightsheet PAINT. Side-note: This paper has what might be the best supplemental section ever, with lots of useful information on Nyquist sampling, resolution, etc.

Chapter 19 – An active contour ImageJ plugin to monitor daughter cell size in 3D during cytokinesis (Paluch lab). Self-explanatory, methinks.

A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy (Fenyo lab – featuring Salk postdoc Dylan Reid, currently in the Gage lab!).

Beyond Cell Toons (Gary Borisy) Wonderful essay by one of my scientific heroes from 2000.

Affimer proteins are versatile and renewable affinity reagents (McPherson and Tomlinson labs). Promising work showing how and why we might want to move away from using antibodies for quantitative fluorescence imaging, including superresolution imaging.

Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing (by Justin Matejka and George Fitzmaurice at Autodesk) – absolutely fantastic visualizations explaining why and how we should be more careful when displaying and reporting our datasets.

In Vivo Ribbon Mobility and Turnover of Ribeye at Zebrafish Hair Cell Synapses (shameless self-promotion). Obviously really cool work showing how one can use a combination of photobleaching and Monte Carlo simulations to determine the dynamics of synaptic structures.

Red fluorescent protein-based cAMP indicator applicable to optogenetics and in vivo imaging (Kitaguchi lab). Always exciting to learn about new and improved genetically encoded fluorescent tags.

Smooth 2D manifold extraction from 3D image stack (Genovesio lab) – Anyone who has ever done a max intensity projection of a 3D stack should take a look at this and try it.

Super-resolution microscopy with very large working distance by means of distributed aperture illumination (Cremer lab) – Fascinating scheme from the Cremer lab.

NanoJ-SQUIRREL: quantitative mapping and minimisation of super-resolution optical imaging artefacts (Henriques lab) – More ImageJ plugins from the Henriques lab to enable and improve superresolution imaging in the wider biology community.

Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy (Boyden lab) – Always keeping a close eye on Boyden’s inspiring expansion microscopy work.

Modeling noise for image simulations (Kyle Douglass) – This is a blog post by a postdoc at EPFL in the Manley lab (who is also a Lippincott-Schwartz lab alum, like yours truly).  This is a useful hands-on introduction to how we should think about noise and image detection.

Electron cryo-microscopy structure of the mechanotransduction channel NOMPC (Cheng lab) – Awesome demonstration of how much we can learn from single particle cryo-EM, in this case a mechanotranduction channel (a topic close to my scientific heart, given its central role in inner ear function).

A DNA origami platform for quantifying protein copy number in super-resolution (Lakadamyali lab) – Nice methods paper showing how to use DNA origami to calibrate your analyses of superresolution images

Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy (Shroff lab) – Hari Shroff is one of the most brilliant microscope developers around, and played key roles in the development of lightsheet microscopy. Here is the latest, showing how to use a third objective for improved lightsheet imaging.

Stay tuned for more!

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