Tag: imaging

Real-time tracking and 2p imaging with sub-ms timing

In this work, the authors used fast optical motion tracking and 2p imaging to measure the activity of individual neurons in freely moving animals. No surgery. No optical window. No restraint. And all the benefits of multiphoton…



Using NI DAQmx in MATLAB

This post is from Rob Campbell:
As part of TENSS we have created a set of examples showing how to use DAQmx in MATLAB without the Data Acquisition Toolbox. This is achieved using…



OpenMV – Fast and easy machine vision

OpenMV is an open source machine vision system. It’s designed to be easy-to-use, with a gentle learning curve. They want this to be the “Arduino of Machine Vision”. The software IDE is free and…



Moire lenses

Moiré lenses are cool: two patterned diffractive optical elements are rotated relative to each other to vary the power of the “lens”. Just watch the video (below).

Demonstration of focus-tunable diffractive Moiré-lenses
Stefan Bernet, Walter Harm, and…



Pixy computer vision for tracking mouse behavior

Pixy is an open source computer vision system. Mostafa Nashaat, Robert Sachdev, and colleagues including Matthew Larkum have developed software for use with the Pixy, that can be used to track mouse behavior, including free movement around an enclosure…



Analysis algorithms: performance quantification and ground truth

We recently tweeted about a preprint from Eftychios A Pnevmatikakis and Andrea Giovannucci (code). The preprint is on motion correction for calcium imaging data. It is a nice quick read and discusses earlier work in the area….



Imaging course at Max Planck Florida

Max Planck Florida is running their imaging course again and there’s still time to apply. They’ve got great faculty including Na Ji, Ryohei Yasuda, Yi Zuo, Chris Xu, Jeff Lichtman, Naomi Kamasawa, and more!



Allen Institute’s Brain Observatory data set

The Allen Institute has released the first set of data from their Brain Observatory project. Many of you already know about this, but I wanted to post about it to encourage people to take a bit…



Ripple noise on PMTs in 2-photon imaging

Andrew Lim wrote in to discuss strategies on dealing with ripple noise in 2-photon imaging systems, particularly when using resonant scanners. He writes:

This isn’t so much a tip as a problem with resonant two-photon scopes that several…



Postdoc position with Duguid in Edinburgh

A world-class in vivo patch clamp electrophysiologist, Ian Duguid, is recruiting to his lab. Ian provides excellent training, and his lab is in a tremendous setting: Edinburgh. Ian’s also one of the current…



3D printed fly holder

Peter Weir has a nice write up and directions on how to make the fly holder from his recent paper. He has some other useful notes that are worth checking out too: github, blog, …



moco, fast open-source motion correction for 2-photon calcium imaging movies

Results are similar to the slow version of TurboReg, but it runs about twice as fast as the fast version of TurboReg.

Here’s the paper.
Here’s the code.



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…



Constrained non-negative matrix factorization for calcium imaging data analysis

I tweeted about this last fall. This is the best algorithm I’ve seen for segmenting and extracting time course from calcium imaging data. Eftychios Pnevmatikakis developed the code in Liam Paninski’s lab. The work is…



CANDLE-J for denoising 2p data

Collaborative Approach for eNhanced Denoising under Low-light Excitation, or CANDLE, is a denoising algorithm specialized for the type of images that are acquired in 2-photon imaging applications. There’s code for both ImageJ and MATLAB available at that…