Driving a green laser pointer with MicroManager

Reminder: green laser pointers have a ton of IR in them. It needs to be filtered out if you don’t want it. See this old (2011!) Labrigger post. I.e., Paul and Kurt are right (see above). The absurd amount of power you measure out of a “green” laser pointer is not because it is recklessly

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Pixy computer vision for tracking mouse behavior

Pixy is an open source computer vision system. Mostafa Nashaat, Robert Sachdev, and colleagues including Matthew Larkum have developed software for use with the Pixy, that can be used to track mouse behavior, including free movement around an enclosure (top image), or track the movement of individual whiskers (bottom image), all at 50 Hz. Here’s

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Analysis algorithms: performance quantification and ground truth

We recently tweeted about a preprint from Eftychios A Pnevmatikakis and Andrea Giovannucci (code). The preprint is on motion correction for calcium imaging data. It is a nice quick read and discusses earlier work in the area. (That’s Eftychios of constrained-non-negative-matrix-factorization-for-calcium-imaging-analysis fame). Marius Pachitariu recognized the algorithm as very similar to one that he uses

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Intan CLAMP Patch Clamp Amplifier Systems

Multiple people have asked for a discussion of Intan CLAMP patch clamp amplifiers. For those who are unfamiliar with them, they’re miniaturized patch clamp amplifiers. What looks like a headstage, is actually an entire amplifier. So that cable out the back of the “headstage” is actually a digital signal, and thus less susceptible to noise.

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The breadboard you didn’t know you wanted

It’s a microcontroller built into a breadboard. Actually, TWO microcontrollers. Both are Arduino-compatible. ATmega16U2 and ATmega328P. It comes in both black, white, and pink because style matters. P.S. The bottom side is filled with Lego connectors. We love Legos, but we bet we’ll never use that feature. Still, it can’t hurt.

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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

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Imaging course at Max Planck Florida

Max Planck Florida is running their imaging course again and there’s still time to apply. They’ve got great faculty including Na Ji, Ryohei Yasuda, Yi Zuo, Chris Xu, Jeff Lichtman, Naomi Kamasawa, and more!

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Pre-preprint: blogging a project

SLAB is trying something new with one project in the lab. Prior to drafting a preprint, we’re blogging the project and sharing the results and analysis. We invite anyone to comment on the work.

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Allen Institute’s Brain Observatory data set

The Allen Institute has released the first set of data from their Brain Observatory project. Many of you already know about this, but I wanted to post about it to encourage people to take a bit of time to check out the data set themselves. They have a github page with materials that can help

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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:  

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ReSpeaker – Funded, still-available kickstarter for adding voice control to your project

In an earlier post, we discussed how surprisingly useful well designed voice control can be. There are open source software solutions for voice control, but they aren’t integrated with hardware, and there wasn’t really a kit to help one get started. Now there is. Here’s an open source kit for adding voice control to whatever

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SLAB is hiring postdocs – neurobiologists and engineers

Just a reminder to anyone looking for a postdoc position: check out the “Now Hiring” link above. We’re looking for people who are pure neurobiologists, pure engineers, or any mixture of the two. Graduate students that are interested in the lab are also encouraged to contact us, especially if they might be graduating soon. We

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Checking PMT performance over time

PMT performance can degrade over time. A friend asked mine recently ask for suggestions on how to check PMT performance. In a prior post, I mentioned that the Hamamatsu PMT Handbook talks a bit about the proper way to make calibrated measurements of PMT sensitivity. If you don’t need calibrated numbers, and just want to

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H.G. Wells and tissue clearing

This passage from H. G. Wells’ The Invisible Man (1897) is an interesting way to introduce the concept of index-matching for tissue clearing. By making sure all of the material interfaces (e.g., lipids, intracellular solutions, and extracellular solution) have the same index-of-refraction, one can render a body transparent. And here is another fact you will

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Postdoc opening in Paris, Schmidt-Hieber lab

Christoph Schmidt-Hieber’s new lab at the Pasteur in Paris will open later this year and he has an opening for a postdoc to study neural circuits for navigation and memory. Labrigger has covered Christoph’s open source work before, on mouse VR and electrophysiology. Here is a link to that part of his web page.

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