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
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:
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
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.
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.
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
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)
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.
George McNamara recently posted a comment on spectra, which referenced this online app which is handy.
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
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
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.
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 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 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
- GCaMP6 now available on
- Sourcing small parts on
- Analysis algorithms: performance quantification and ground truth on
- Laser pointers and quantum mechanics on
- Pixy for easy Arduino machine vision on
- Constrained non-negative matrix factorization for calcium imaging data analysis on
- Series resistance in patch clamp experiments on
- Checking PMT performance over time on
- GCaMP6 reporter mice on
- GCaMP6 reporter mice on
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