source: C&H

Undocumented MATLAB has an in depth look at the next generation graphics handler for MATLAB which you can use today, although it’s not officially released yet. Use the command line option “-hgVersion 2″ when launching MATLAB. See the post for more details.

Here’s a follow up on the previous post about alternatives to Google Reader (which is being shut down).

Patrick Mineault commented that Feedly is looking good. I agree. Basic functionality is smooth and somewhat intuitive; layout and design are excellent.

Magazine view

Cards view

Post by Jeffrey Stirman

The opacity of the brain is one barrier to optically imaging individual neurons and their connections. Scattering in tissue is the main reason tissue is not transparent; absorption also plays a role but much less so. Perfusing tissue with a substance to match the index of refraction throughout the preparation (and thus decrease scattering) is one approach, and although index matching isn’t a new strategy, just getting rid of the membranes is. The most recent method to achieving tissue transparency (Chung et al., 2013), takes this approach to great effect.

A nice paper discussing tissue transparency is Johnsen and Widder, 1999. Scattering in tissue is dominated by Mie scattering which is the scattering of light by particles of a size on the same order as the wavelength of light (Rayleigh scattering is for particles much smaller than the wavelength): cells, nuclei, and organelles all fit in this category. Furthermore, the lipid membranes encasing these structures have a significantly different refractive index (~1.5) than the surrounding medium. It is this change in refractive index of these particles that lead to scattering. Simply, as the difference in refractive index between the surrounding medium and the object increases, so too does the scattering. The relationship with wavelength can be complicated and range from about lambda^-4 to lambda^0.2 (lambda = the wavelength of light used) depending on the size of the particle, but overall the higher the wavelength, the less scattering (one of the benefits of 2-photon imaging).

A couple of nice papers from Mourant et al. (1998 & 2000) discuss and explore in more detail the dominant scattering centers in tissue. They found that at small angles, most of the scattering was dominated by the nucleus and at larger angles the smaller structures such as mitochondria. One conclusion from all this is perhaps it might not be sufficient to homogenize the refractive index of the tissue if those lipid membranes still exist (as earlier attempts had done). In fact, the best way to achieve tissue clarity for imaging is to remove the objects that cause the scattering. This is exactly what Kwanghun Chung did! By first crosslinking most of the proteins, DNA, and other biological entities (not the lipids), then cross-linking them all in a hydrogel structure, he was able to use a detergent extraction process (electric field assisted) to remove the lipid membranes and thereby removing the cause of most of the scattering centers. Since multiple rounds of antibody staining can be performed on the cleared tissue, this process seems to have achieved clarity while preserving most of the interesting biology.

Previously…
Sense of scale
R&D budgets in perspective

Google Reader is going to be shut down on July 1.
If you use Reader, here’s what to do:

Step 1: Export all of your subscriptions from Google Reader
(takes less than 1 minute)

Try these directions. It’s easy.

Step 2: Start using an alternative, and import your old Google Reader stuff.
(can take as little as 2 minutes, once you decide on one)

I’m trying Bibliogo right now, and I like it so far. It’s geared towards academics, so it’s a good fit for the Labrigger audience. It opens webpages within the window in a nice way, making it fairly quick to flip back and forth between RSS entries and the actual webpages. Even Google Reader never did that very well.

But there are other alternatives.
WordPress has a Google Reader-like feature.
SmashingReader looks nice.
If you have your own server, you might like Fever or PrivateOSS.

xcorr has done a nice series of reviews of IDEs for scientific Python: First, Second, Third

Previously
Online scientific Python
NEURON and Python

More open source software to check out.

Two-Photon Processor and SeNeCA – A freely available software package to process data from two-photon calcium imaging at speeds down to several ms per frame.
Jakub Tomek, Ondrej Novak, and Josef Syka
TJ Neurophysiol published 10 April 2013, 10.1152/jn.00087.2013

It’s notable in that it is an “all-in-one” package that’s freely available.

The image processing to detect cells and draw ROIs seems to work pretty good, even with poor S:N. I’d like to see it operate on GCaMP images, since those are more challenging in some ways. Cells labeled with Oregon Green BAPTA-1 tend to exhibit spherical patterns of somatic fluorescence, but GCaMP, when it’s working well, does not brightly label the nucleus, so the shape of the ideal ROI is quite different. Plus, it’s nice to pick up dendrites and other features, not just somata.

See also, Vogelstein’s code for inferring action potentials in calcium imaging data.

Hat tip to Christian Wilms
EDIT: The code became available shortly after this post.