Category: Signal processing

• Sorting calcium imaging signals

  Calcium imaging can record from several dozens of neurons at once. Analyzing this raw data is expensive, so one typically wants to define regions of interest corresponding to cell bodies and work with the average calcium signal within. Dario has a post on defining polygonal ROIs using the mean fluorescence image. Doing this manually is fairly time-consuming and it…

  October 3, 2014

• Non-rigid deformation for calcium imaging frame alignment

  Following my PhD at McGill, I moved to LA to work in Dr. Dario Ringach’s lab at UCLA. We’ve been doing calcium imaging – GCamp6 – in mice via a custom-built microscope – you can read more about the microscope over at the Scanbox blog. If you’re used to working with single electrodes or multi-unit…

  August 2, 2014

• Whiten images in Matlab

  Previously, I showed how to whiten a matrix in Matlab. This involves finding the inverse square root of the covariance matrix of a set of observations, which is prohibitively expensive when the observations are high-dimensional – for instance, high-resolution natural images. Thankfully, it’s possible to whiten a set of natural images approximately by multiplying the…

  April 30, 2013