Category: Tips

Server space – cloud or on-campus?

Cloud storage is not the cure-all it is sometimes proposed to be. On-campus servers have some advantages in transmission speed and cost, especially as storage requirements grow considerably. Talk to your campus IT services before shelling out 90% of your R01 to Amazon to store your petabyte (PB) dataset. Cloud storage is good for personal

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

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

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!

Tons of 2p spectra –

  Daniel Fiole is curating a nice resource for 2p cross sections: 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:  

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

Ripple noise on PMTs in 2-photon imaging – Part 2

The recent post on ripple noise generated some comments and additional discussion. Go check out the comments on that post. For example, Peter Rupprecht shared some snapshots an oscilloscope display showing the signal from the BNC connector at the back of the laser, in the presence of this ripple noise. The ripple is seen when

Ripple noise on PMTs in 2-photon imaging

Andrew Lim wrote in to discuss strategies on dealing with ripple noise in 2-photon imaging systems, particularly when using resonant scanners. He writes: This isn’t so much a tip as a problem with resonant two-photon scopes that several people have told me they also have but I haven’t seen a solution for (other people apparently

Slack software for labs

Slack is very useful team coordination software. It’s been such a help in my own lab, that I suspect that given a properly configured Slack account, I could simultaneously run GE, Google, Intel, and the US Federal Government. It’s easy to dismiss Slack. To a large extent, it’s basically a bunch of chat rooms. I

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.

Phase retrieval

Microscopists are often adapting techniques pioneered for astronomy. Adaptive optics is the example you all probably know. Relatedly, phase retrieval was originally developed for telescopic imaging systems, and was adapted for high NA microscopic imaging systems by Mats Gustafsson and colleagues (Hanser et al. 2003 Optics Letters). A couple of excellent optics people, Kyle Douglass

Upconversion: NIR in, vis out

Compared to visible (vis) light, near infrared (NIR) wavelength scatters less and is less absorbed in brain tissue. If your fluorescent target absorbs vis light, then one way to use NIR is to flood the area with molecules that will absorb NIR and emit vis light. The process is called “upconversion“, since it is in

Cute trick for spinning down tubes

The web site is in Japanese, but the pictures and gif are self explanatory.

Voice control

Voice control has just recently become interesting to me. Ikuko bought me an Amazon Echo and I’m surprised at how useful I find it. I’m also surprised at how well it works– it can decipher my commands even when I’m whispering or mumbling from across the room. But the usefulness is what surprised me the

Clearing out a gmail account

If your gmail account gets filled up and you need more space, you could pay for an upgraded gmail account with more storage. Or you can clear out space. For clearing out space, there are two approaches: The surgical option: Delete large emails to free up space. The search arguments “has:attachment” and “larger:30mb” (or “larger:10mb”,