Raspberry Pi 2 and Pi B plus kits for cheap
Posted in Hardware
SIMA update – for 2p calcium imaging
Posted in Software
SIMA has recently been updated (here’s the original Labrigger post):
From the SIMA team:
We have recently released updated versions of the SIMA & ROI Buddy tools for analysis of calcium imaging data (motion correction,…
NES – NeuroMat – browser-based data collection
Posted in Software
NES, from NeuroMat, is an open-source tool to manage clinical data gathered in hospitals and research institutions. Here’s their github link. More info from the lab.
…
3D printed electronics
Posted in Hardware
It’s been promised for a while now, but someone has to do the hard work to make it happen. That inevitably involves some pretty pitiful looking stepping stones on the way to the…
Proper export for MATLAB figures
Posted in Software
Getting nice figures out of MATLAB can be a challenge. Sometimes it’s fine, but if you’ve hit upon a figure that simply isn’t exporting nicely (bad vector rendering, lost transparency, etc.), check out the…
Colorbrewer for color schemes
Posted in Tips
Colorbrewer was designed for cartography, but is useful for figure color schemes and look up tables (LUTs). The web interface is slick, offers an immediate preview, and the look up table can be exported….
Time-bandwidth product
Posted in Software
Ultrafast pulses are formed through interference of different wavelengths of light. Think of Fourier transforms, and how pulses can be generated through constructive and destructive interference of wavelengths with aligned phases. These wavelengths are close to the center wavelength, and spread over a wavelength…
Arduino + x86 power
Posted in Hardware
The Intel Galileo is an interesting mashup. It’s Arduino compatible. You can hand it to an undergrad and they can download the Arduino IDE and program it on their own with relatively little training….
Practical guide to optical alignment
Posted in Tips
This is a nice, quick, and practical introduction to optical alignment. A good place to start for training. By Rainer Heintzmann.
…
Python ephys and calcium imaging analysis code
Posted in Software
Andrew Giessel wrote some analysis code in Python when he worked in the Datta lab. He has since moved on to another venture, but he open-sourced the code. There are import routines for data from…
TriggerScope for imaging system device control
Posted in Hardware
Austin Blanco has designed and built an open-source system for controlling complex imaging systems called TriggerScope. It’s highly customizable out of the box, and both the firmware and software are open.
Olympus 10x for two-photon microscopy
Posted in Hardware
Olympus released a suite of new objectives this year, and one of them is this 10x/0.6 NA. This is probably the longest focal length (180/10 = 18 mm) objective you can get and use…
How to wrap cables
Posted in Tips
I like things clean and organized. I’m basically Martha Stewart. With more lasers and fewer indictments.
Depending on the length of the cord and its minimum bend radius, several different wrapping styles can be acceptable. Here…
Rube Goldberg machine using light and optics
Posted in Uncategorized
It’s an ad for a Japanese company’s fiber optic network. In the US, we call these Rube Goldberg machines. In Japan, they’re called Pythagorean Switches (actually). In the UK, they’re called Heath Robinson machines.
…
Patch clamp amplifier in chip form
Posted in Hardware
See that metal box the pipette holder is attached to? That’s not a headstage, that’s the whole patch clamp amplifier. Reid Harrison is the lead author (co-senior authors are Craig Forest and Ed Boyden)…