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Learn how to effectively use the watershed algorithm for spike sorting by plotting raw data and modifying feature space in MATLAB. Follow this step-by-step guide for efficient analysis.
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Apples From Mathworks
Computer Finds Apples From Mathworks
Quick reference guide to watershed add on: Installation: • Go to website koulakovlab.cshl.edu/watershed and download Mclust.zip • Unzip it to any directory • Include directory AND ALL SUBDIRECTORIES into matlab path • Type MClust at the MATLAB prompt • You are ready to go
USAGE • In the main MClust window select additional features ud like to use • PCApeak – PCA on the maxima for each channel • PCAwave – PCA on the voltage profile • PCAshft – PCA of the voltage shifted so that the maximal voltage for an event is in the middle of the profile • PCAchsh – PCA on voltage shifted that the maximum of voltage FOR EACH CHANNEL is in the middle (individual time-shifts for each channel) • Press View Clusters 3D
Watersheding • USE PCApeak components (2,3,4) for best results • Press Watershed button • Examine the voxelated density using the interface • Close the interface for proceed further
Filtering data • When asked about the smoothing size respond (2-5 is best) • When asked about high-pass filter size respond (3-5 is best). Type 0 for none • When asked for the depth of the marker type a number btw 0 and 1. type 0 for no marker based WS. The value of 0.1 is acceptable in most cases. • Wait a few seconds. • Type Update Clusters • Type Redraw Clusters • Enjoy!
Acknowledgements • Dr. Koulakov • Mainen Laboratory (recording data) • Spike-Sorting scientists • CSHL administration