Category Archives: Data analysis

High quality time series plots

Posted on February 15, 2016 by jvoigts

What is the best, or at least a good way to plot time-series data on a screen? When dealing with time series data in electrophysiology, a good deal of time is spent looking at plots in order to judge data … Continue reading →

Posted in Data analysis, Electrophysiology, Open Ephys | Comments Off on High quality time series plots

Fast approximate whisker tracking in the gap-crossing task

Posted on December 1, 2015 by jvoigts

After finding the mouse’s nose position (see post on Tracking mouse position in the gap-crossing task), I wanted to get a fast, robust estimate of the basic whisking pattern, together with approximate times when whiskers could have been in contact with … Continue reading →

Posted in Data analysis, Matlab | Leave a comment

Tracking mouse position in the gap-crossing task

Posted on November 28, 2015 by jvoigts

This post is a quick walk-through of some code I recently wrote for tracking rough mouse position and a few other things in high-speed video in a gap-crossing task. This code is just very basic image processing, ugly hacks and … Continue reading →

Posted in Data analysis | Comments Off on Tracking mouse position in the gap-crossing task

Maintaining local pixel cross-correlation in image registration

Posted on March 30, 2015 by jvoigts

This post is about the effect of re-sampling in image registration methods on local pixel cross correlation for analyzing calcium imaging data. In awake 2p imaging, animal motion causes brain tissue motion and image motion. While z-motion that can not be recovered … Continue reading →

Posted in Calcium imaging, Data analysis, Matlab | Comments Off on Maintaining local pixel cross-correlation in image registration

Localizing recording sites: Reconstructing explanted electrode arrays

Posted on April 11, 2013 by jvoigts

While drive implants with adjustable electrodes bring many advantages, the use of movable electrodes adds one element of uncertainty to the data analysis: the precise depth of each electrode is not known with absolute certainty during recording. By identifying landmarks along the … Continue reading →

Posted in Data analysis, Electrophysiology | Comments Off on Localizing recording sites: Reconstructing explanted electrode arrays

Template matching in manual spike sorting

Posted on March 13, 2013 by jvoigts

When sorting spikes, it is pretty common to find a bunch of nice example waveforms for a unit, but it is often tricky to find good features that cleanly separate these waveforms from the rest. For this reason, many clustering packages can … Continue reading →

Posted in Data analysis, Matlab, Technical things | Comments Off on Template matching in manual spike sorting