Commoditizing population calcium imaging analysis

More open source software to check out.

Two-Photon Processor and SeNeCA – A freely available software package to…



Variability where you really don’t want it

Post by Christian Wilms

I’ll admit it: I’m lazy. When I use a calcium indicator and need to know its physico-chemical properties, I like to simply look it up in the manufacturer’s catalogue or…



New Orleans

While they’re at it, let’s go back to Miami too.



kawaii psychophysics

Apparently kittens can see an optimized Farser-Wilcox optical illusion.

Fraser and Wilcox 1979 (pdf)
Rotating Snakes (pdf)



Online brain atlases

INCF’s brain atlases (mouse, macaque, and human) are easy to browse online. The system has been around for several years now, and keeps getting better.

Of course, the Allen Institute also maintains some excellent…



1000 words

Randall Munroe did an xkcd cartoon a while back where he tried to explain a Saturn V rocket using only the 1000 most common words in English. The resulting work, entitled “Up Goer…



Cough syrup

My MD friends tell me there’s no effective cough medication on the market. There are OTC and prescription medicines, but none of them have been proven to really work. That doesn’t mean that they won’t give you some level of subjective relief, but they’re not like asprin or pseudoephedrine (e.g., regular Sudafed)*.

We used to…



Imaging deeper with 3p

One of the factors that limits the depth at which one can image brain tissue in vivo with two-photon imaging is out-of-plane fluorescence. Although the excitation falls off as the square of the distance from…



Converting miles to km with Fibonacci

Previously on Labrigger: Street fighting mathematics

And on that topic, and this is something the runners among us might appreciate, the Fibonacci sequence can be used to easily convert miles to kms.

Take two consecutive…



Going back to Cali

No. I don’t think so.
Anyways, CaliCode is a resource for population calcium imaging. It covers topics from inferring action potential trains from imaging data (hat tip to JV), to image processing and topical…



Methods of Mayhem

I’ve seen this line in a methods section before:
“Experiments were carried out at room temperature (19-29 degrees C).”

Which means: “Our lab is in a building with no A/C and poor heating.”

For…



More references

Wolfgang Becker just gave a nice talk at the Berkeley Advanced Imaging Methods meeting.

I should add the Becker-Hinkl literature to the list of online references.

Previously
Catalogs as textbooks
Troubleshooting fluorescence microscopy



PubPeer Anonymous

You can now post comments on PubPeer completely anonymously. Not even a login is required.

PubPeer has always allowed anonymous comments, but it used to be that you had to log in, so the…



Markram’s Millions

Henry Markram got his wish. He was just awarded 500,000,000 Euros to build a computer model of the brain. In NIH terms, that’s over…



Electrophysiology software

Unenthusiastic about spending thousands of dollars on electrophysiology software like pCLAMP? Try the free and open source Strathclyde Electrophysiology Software. It’s a suite of programs for recording and analyzing signals from intracellular electrophysiology…