I find WPI’s Kwik-Cast handy for some things around the lab. When we were modest users, the price didn’t bother me too much. However, when we started going through so much of it, I wondered if there was a way to buy it that fit our consumption level a bit better.

Both of those pots together were about $50. (Body Double Fast Set – Trial Size, Reynolds Advanced Materials)

These are the double-barreled syringes and mixing tips I bought. They’re from this company.
2mm x 8 Element, Needle Tip
qty. 1-99 – $0.91 each (WPI charges about $2.90 per tip, about 318% more)
qty. 100+ – $0.637 each (Buy 100 for $63.70. From WPI, 30 tips cost $87.00, 455% more)

4B19 Double barreled syringe
qty. 1-99 – $1.953 each
qty. 100+ – $1.367 each

Here, you can see below that the WPI Kwik-Cast kit uses the same syringes and mixing tips, at least as far as I can tell.

From WPI, each of these syringes (with contents) is $85.

So you can buy the DIY stuff above ($50), 50 tips ($9.10 * 5 = $45.50), and 10 syringes ($19.53) for a grand total of $115.03. This would cost $850 + ($29 * 5 = $145) = $995.00 from WPI.

Plus, with the DIY way, you’ll still have the vast majority of your silicone elastomer left over from the $50 kit. I’m not sure I’ll ever run out.

The drawback of the DIY way is that you have to fill your own syringes, or have an undergrad do it for you. I used a couple of 5 mL syringes, and it took maybe a minute or two to do one syringe.

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