Tag: microscopy

Democratized state-of-the-art neuroscience

Andre and colleagues have a preprint up on their project generating inexpensive instrumentation for imaging and optogenetics experiments. The 100 Euro Lab: A 3-D Printable Open Source Platform For Fluorescence Microscopy, Optogenetics And Accurate Temperature Control During Behaviour Of Zebrafish, Drosophila And C. elegans. The authors use this instrumentation in courses at African universities. Open

Driving a green laser pointer with MicroManager

Reminder: green laser pointers have a ton of IR in them. It needs to be filtered out if you don’t want it. See this old (2011!) Labrigger post. I.e., Paul and Kurt are right (see above). The absurd amount of power you measure out of a “green” laser pointer is not because it is recklessly

Checking PMT performance over time

PMT performance can degrade over time. A friend asked mine recently ask for suggestions on how to check PMT performance. In a prior post, I mentioned that the Hamamatsu PMT Handbook talks a bit about the proper way to make calibrated measurements of PMT sensitivity. If you don’t need calibrated numbers, and just want to

Open source structured illumination MATLAB code

Peng Xi (Peking University) shared this resource his lab has developed: software for processing images for structured illumination (a superresolution technique). Here’s the Github repository. And here’s the paper (pay wall). Previously on Labrigger… Structured illumination Notes from an email exchange with the late Mats Gustafsson, a pioneer of structured illumination microscopy

2-photon calcium imaging of the mouse retina in vivo

Bar-Noam et al. 2016 (Shy Shoham’s lab) figured out how to image the mouse retina with 2-photon microscopy in vivo.

Open source head-mounted calcium imaging

The UCLA Miniscope project is an NIH BRAIN Initiative-funded project to open source head-mounted calcium imaging devices. Their web site is online now. They’ll be releasing all of the information needed for making these devices yourself, including data analysis. They’ll also be holding workshops to train users. These devices compare favorably to commercial options. Inscopix

CodeV, Zemax, OSLO, or …

Trying to decide which optical design software to use? Just try them out and decide for yourself. I like how Steve Eckhardt (great guy, btw, in case you’re looking for someone to consult with) summarized their different strengths: “CodeV’s Global Synthesis is an extremely powerful global optimizer while Zemax makes it easy to take control

TriggerScope for imaging system device control

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

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 with a standard two-photon system and see activity in single neurons. 0.6 NA might not be enough for tissue bulk labeled

Field of view = 3.5 mm with cellular resolution

In this preprint, Stirman et al. report achieving a 3.5 mm field of view with 2-photon excitation with cellular resolution. The design involves custom scan optics and a custom objective built in the SLAB. It’s an air immersion objective with about a 9.5 mm working distance. Rapid dissemination is a priority. If you’re interested, contact

A Canadian open source two-photon microscope system

This open source two-photon microscope system is adaptable for both slice (with substage detection) and in vivo experiments, and is built with largely COTS parts. The paper is a very nice resource. See also, designs shared by the Svoboda lab

Notes from Austin Blanco

Our friend Christian Wilms tipped us to Austin Blanco’s blog, which has some posts you all might be interested in: Characterizing unknown optical components A few notes on Arduinos, their timers, and using them with rotary optical encoders Long-term considerations when buying or building and imaging system Surprisingly clean +/- 5 volts from USB or

Reminder: SfN Short Course

If you like Labrigger, you should register for this Short Course at the SfN meeting. Short Course #1: Advances in Multineuronal Monitoring of Brain Activity Spencer Smith will be talking about the work SLAB has been doing designing and building custom optical systems for wide field of view two-photon imaging. These recent comments provide a

Custom scan optics for two-photon imaging

Adrian Negrean, in Huibert Mansvelder’s lab, has been designing and building custom scan optics for two-photon imaging and earlier this year published his work (paper). Labrigger wants to emphasize how nice this paper is. It’s an easy read, with clear figures, and offers a lot of practical insights. It has a ton of information and

OpenLabTools at Cambridge

OpenLabTools is a new initiative at Cambridge University, using engineering students to develop modular lab equipment. The OpenLabTools initiative aims to provide a forum and knowledge centre for the development of low cost and open access scientific tools, with an emphasis on undergraduate and graduate teaching and research. The programme is developed thanks to contributions