Wakari Bundles – standardized Python for sharing code

I’ve been using Spyder recently for a MATLAB-like Python development environment (thanks for the tip, xcorr!).

For python development within a browser window, I’ve used Wakari a bit. Now they have Bundles,…



X-ray crystallography of cookies

This is perhaps the most exhilarating patent I’ve ever read:

Search for patent 4455333 at this link.

Here’s a excerpt:

When the cookie dough enters the oven, the water in the dough is saturated with sugar and appears to be evenly distributed throughout the dough. As the water temperature…



Pulsed laser power part 2

In a previous post, we discussed how peak power is computed. Although Ti:Sapph laser manufacturers typically quote the average power, peak power is the more relevant quantity for two photon excitation. Here’s a graph…



Optogenetics scattering iOS app

Here’s an iOS app which is basically a scattering calculator to help plan optogenetics experiments. There are also some plates from a brain atlas.
(via the OpenOptogenetics blog)



Waterloo graphics for MATLAB

Undocumented MATLAB has another post on improving graphics in MATLAB (previously). Waterloo is an easy-to-install package that generates nice graphics using Java. It can be used with MATLAB, R, and other software.



OpenSPIM and OpenSpinMicroscopy for light sheet microscopy

This month, Nature Methods highlights a couple of open light sheet microscopy…



GNOOM for spherical treadmill VR

Mice can learn to navigate virtual reality environments using a spherical treadmill, and this behavior drives place cell and grid cell activity.

Christoph Schmidt-Hieber has started uploading his code to Google….



Superhydrophobic spray-on coating now available

Neverwet is now available for about $20.

This is a spray-on, 2-part superhydrophobic coating (translucent when dry). What would it be useful for in a lab? For starters, spraying it on anything that needs to be cleaned regularly might make it easier to clean. Also, it can…



Local cross corr images

One key step in analyzing data form calcium imaging experiments is segmentation (i.e., drawing regions of interest, ROIs). There have…



MATLAB 2013a natively supports Kinect

There have been wrappers for interfacing with the Kinect device before, but the latest update to MATLAB makes it native to the Image Processing Toolbox. source

Drop a Kinect…



Trimming pipette tips

I saw Benjamin Judkewitz trim the fat end off of a pipette tip and stick it onto a 1 mL syringe to make a fine tip for the syringe (above). This is handy for…



A clinic in figure design

You don’t have to be an APBRmetrician to appreciate the graphics Kirk Goldsberry puts together from his analysis. They’re clear, the data-to-ink ratio is high, and there are appropriate…



The San Francisco Declaration on Research Assessment (DORA)

“The Journal Impact Factor, as calculated by Thomson Reuters, was originally created as a tool to help librarians identify journals to purchase, not as a measure of the scientific quality of research in an…



PubPeer catches image reuse in Cell paper



Cheap DIY Kwik-Cast

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…