Tag: references

Series resistance in patch clamp experiments

For teaching electrophysiology, there’s still a lack of comprehensive references. In particular, it can be difficult to impart to students an intuitive feel for the quality or fidelity of electrophysiological recordings. How close to the truth are those traces you just recorded? This sort of practical discussion is often touched upon in electrophysiological texts, but

Tons of 2p spectra – twophotondyes.com

  Daniel Fiole is curating a nice resource for 2p cross sections: twophotondyes.com There’s a lot here. It’s not just dyes, he has links for fluorescent proteins as well, and there’s 3p data linked to as well: Prior posts on 2p cross sections:  

iPad/iPhone/iOS app RayLab for optical design

RayLab is an iOS app (iPhone/iPad) for optics analysis. It has some nice features– more than I expected. It’s a nice piece of work! For many practical applications it cannot replace conventional optic design software (e.g., Zemax/OSLO/CodeV). That said, it’s a very interesting product and worth checking out. It also does ACBD matrix analysis. Here

Enhancer trap mice from Brandeis

There’s a project in Sacha Nelson’s lab at Brandeis to generate and characterize enhancer trap mice for studying neural circuitry. They have a nice online searchable database of the lines they’ve generated, complete with histological sections and methods.

New category of posts: papers

In the past, Labrigger has only rarely posted about relevant papers. That ends today. Now there’s a new post category for papers, and it’ll be used to highlight publications that are of potential interest to you, the community.

Lens designs

In the talk I gave at the Short Course at SfN 2014, I briefly discussed the process of optical system design. A common strategy is to start with a published design, or at least a general scheme (series of lens types), and then make modifications to fit the target application. Finding these published designs can

Photonics Handbook online reading

When you run out of catalogs to read, Photonics has some nice short articles. It’s all pretty basic, not too complicated. Good for training (e.g., Optical design software, Fiber lasers)

Practical guide to optical alignment

This is a nice, quick, and practical introduction to optical alignment. A good place to start for training. By Rainer Heintzmann. Hat tip to a recent discussion on the confocal listserv.

Online app for comparing fluorescent proteins

George McNamara recently posted a comment on spectra, which referenced this online app which is handy.

A Canadian open source two-photon microscope system

This open source two-photon microscope system is adaptable for both slice (with substage detection) and in vivo experiments, and is built with largely COTS parts. The paper is a very nice resource. See also, designs shared by the Svoboda lab

Notes from Austin Blanco

Our friend Christian Wilms tipped us to Austin Blanco’s blog, which has some posts you all might be interested in: Characterizing unknown optical components A few notes on Arduinos, their timers, and using them with rotary optical encoders Long-term considerations when buying or building and imaging system Surprisingly clean +/- 5 volts from USB or

Abbe Diffraction setup

Kurt Thorn shared the parts list for his Abbe diffraction setup. He describes how to use it in his blog post, but you can also check out his talk.

Measuring the junction potential

How to measure the liquid junction potential This is an old blog post, but the comments section is still somewhat active. Handy reference/training material.

Software Carpentry teaching programming and data management to scientists

Software Carpentry teaches scientists how to program and use open source tools to manage their data and make their life easier. They’re focussed specifically on software tools, rather than types of analysis, and so what they teach is pretty general. They started in 1998 and are currently part of the Mozilla Foundation. They hold bootcamps,

PubPeer browser plugins for PubMed

PubPeer has released browser plugins that add a line to PubMed results if there are comments on PubPeer for those publications. It looks like the example above. The install took less than 10 seconds. More on PubPeer