Democratized state-of-the-art neuroscience

Andre and colleagues have a preprint up on their project generating inexpensive instrumentation for imaging and optogenetics experiments. The 100 Euro Lab: A 3-D Printable Open Source Platform For Fluorescence Microscopy, Optogenetics And Accurate Temperature Control During Behaviour Of Zebrafish, Drosophila And C. elegans. The authors use this instrumentation in courses at African universities. Open

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March for Science – Apr 22

OSA – Optical Society of America SfN – Society for Neuroscience March for Science

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Nature is diluting their brand

From MIT. Hat tip to J.S. More print-outs: Flyer in the Physics building Kawaii psychophysics

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Actually useful comments on scientific blogging

I came across Rachel Thomas’ comments on blogging in the context of machine learning, and they’re good. I’ve been telling people things like this for awhile now and Rachel distills them better than I do. I’ll quote some of my favorites, but check out her post to read the full story. This single point was

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PMT power supply

I was cleaning house a bit, and among my old files I found this, which might be worth sharing. Years ago I made a centralized power supply for a custom 2-photon imaging system I built. There were two epi detectors (for red & green fluorescence) and three trans detectors (red, green, and IR-based “DIC-like Dodt”

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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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