Bayesian mixed effects model to estimate experimental parameters

I ran into a tricky problem while analyzing a series of experiments we recently performed with Scanbox. We’re trying to estimate the angle of the objective with respect to the cortical surface. The way we approach this is by scanning at a given depth, going down a little bit, scanning again, and so on. By … More Bayesian mixed effects model to estimate experimental parameters

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 … More Sorting calcium imaging signals

Non-rigid deformation for calcium imaging frame alignment

It’s been a while since I last updated the blog – I graduated from McGill, went on a trip to Indonesia where I did a lot of diving (above), came back to Montreal for 16 hours to gather my coffee machine and about three shirts – all I need to survive, really – then moved to sunny California to do a postdoc in Dr. … More Non-rigid deformation for calcium imaging frame alignment