In two previous posts I shared some MATLAB code to help design collection optics in 2p scopes.
Collection optics for 2p scopes, post 1
Collection optics for 2p scopes, post 2
It was just brought to my attention that I didn’t include the command locateVal in the code I posted. It’s a very simple little shortcut I use. Here it is:
function [pos difference] = locateVal(val,data) [difference pos] = min(abs(data - val));
Yes, you could have guessed that. But I wanted to correct the oversight.
Here’s a BCG Matrix for scientific papers. One paper is plotted on the graph. At Nature’s Action Potential blog, the editor explains why they accepted it. This is an interesting step towards greater transparency. Where do other papers you like lie on this graph?
(Hat tip to JT)
On the topic of iOS apps, MATLAB has released v3.0 of their mobile app. The most apparent changes are UI usability improvements.
(MATLAB link, App Store link)
Zeiss released an iOS app for viewing spectra.
No Android version yet, but Johannes Amon said:
of course I can’t tell you any specifics but at the moment we are evaluating a native port to
android ICS 4.0. at the end it always comes down to budget so it would help immensely if
you’d order some confocals right now ^^just joking, gonna keep you posted on this project
It uses George McNamara’s Pubspectra database. (link)
Success rate for all grants at NIH in 2011 = 18 %
Success rate for New Investigators = 15%
More stats at Sally Rockey’s blog.
This site has a nice big list of software for visual psychophysics. It’s very extensive and includes free as well as commercial solutions: visual stimuli, analysis, teaching, hardware, and more.
Virtual desktops are used to manage screen real estate. A user might have a bunch of web browsers open on the desktop, and then hit a key to switch to a nice clean desktop (the web browsing windows are kept in memory). This second desktop can then be filled with image analysis program windows. A keystroke later, and the user is back to the first desktop with the web browser windows, just as they left them.
It’s good for organizing work, which is good for productivity.
If you’ve used OS X sometime in the past 5 years, you might have become accustomed to using Spaces (or the current Mission Control). And those of you who don’t use OS X but have used any varient of Unix sometime in the past… well, just about ever, then you also may have become accustomed to using virtual desktops. Actually, the Amiga 1000 was the first to implement this feature, in 1985.
Somehow, Windows has managed to make it 2012 without a built-in function to support virtual desktops. Unfortuantely, many of the third party alternatives are not all that great, and some are even hardware dependent (e.g., Nvidia’s nView). But there are a couple of free programs that are worth recommending.
mdesktop is what I use. It’s a small, unobtrusive program with customizable keyboard shortcuts.
Desktops is available from Microsoft. Advantage over mdesktop? It offers a little preview of the active desktops when you click on the icon, in case you’re not sure which desktop you want to switch to. However, it also has several disadvantages compared to mdesktop. It’s slower to switch desktops, it changes graphics mode on alternative desktops (Aero is off), and it offers no way to quit the application (you have to kill the process manually and it’s hidden from the active application list).
I’m optimistic that Windows 8 will finally have a good virtual desktop manager. But I don’t have a good reason to think that. I just think Metro looks nice.
On the topic of MATLAB learning materials (covered previously here and lots more MATLAB stuff here), MIT has some online courses freely available. Here’s an “aggressively gentle” intro to MATLAB, and some more MATLAB resources. (Hat tip to MH)
Also here’s a link from an older post on xcorr (Patrick Mineault’s excellent blog). This course webpage has a bunch of examples in MATLAB code. They’re great for simultaneously learning MATLAB and visual neuroscience.
ScanImage is an excellent software package for controlling 2p scopes. It’s free and open source. It’s been actively developed and released to the public since its inception. RIght now they personnel involved are trying to renew their funding. To help keep this resource actively developed and free, please fill out their survey. It’s very, very short. Don’t take the resource for granted. It takes a lot of salaried time to keep the development going and adding in new features.
By the way, ScanImage 3.8 (new features) and 4.0 (for ThorLabs scopes) are out now (3.5 and 3.6 are no longer supported; 3.7.1 is the current stable release) (link). If you haven’t already tried a new version of ScanImage out, you should. It doesn’t take too long and the feedback is very helpful. Don’t assume that everyone else is already sending in the same feedback.
The lasers used in multiphoton imaging deliver their photons in pulses. Many commonly used systems pulse at 80 MHz. However, there are good reasons to try different frequencies.
In 2007, Donnert, Eggeling, and Hell published a Nature Methods paper where they used low frequency pulses to get more fluorescence signal out of the preparation. The idea was that many molecules get excited into triplet states that are long-lived. By having a long time between pulses, there is time for the molecules to fall back down into the ground state so that the next pulse will have a large population of molecules available to be excited.
The next year, Ji, Magee, and Betzig published a Nature Methods paper where they used high frequency, low power pulses to get an increase in signal-to-noise ratio with two-photon imaging.
Several people have been confused by these apparently contradictory results. Recently there was a discussion on the Confocal Listserv about this topic, again pointing out the differences between the two papers.
Andrew Ridsdale chimed in with his thoughts (link to post). One of his points is that n different experiments, different factors are limiting the signal.
In Hell’s experiments with low pulse rates, they were imaging cell-free molecules– a very bright signal. Bleaching (triplet-state occupancy) was the limiting factor, rather than damage. Because there weren’t even any cells around to be damaged, other than E. coli cells in the last figure. So allowing for relaxation time and maximum occupancy of the ground state gave the best results. All of the relevant processes were governed by 2p excitation and thus were second order.
In the Ji, Magee, and Betzig experiments, the signals were very dim and the limiting factor was damage to the preparation. Andrew’s point seems to be that in this case, the signal is coming from second order processes and the damage is from higher order processes, maybe even as high as 5th order, though they estimate it to be on average about 2.4 order. So in this case, it’s best to use pulses that are just barely effective for 2p excitation and completely ineffective for higher order processes (damage), and then blast the prep with as many pulses as possible. Since the likelihood of a 2p event is already low, bleaching isn’t as much of a factor.
(btw, Brain Windows did a very nice post on the Ji and Donnert papers)