Code & DataThese repositories are intended for general use and maintained:
Neuropixels trajectory explorer MATLAB-based GUI to plan Neuropixels trajectories using the Allen CCF mouse atlas. I demo an earlier version of this tool in this video for the 2021 UCL Neuropixels course.
Histology atlas alignment and processing A simple MATLAB pipeline to analyze histology images (including extracting Neuropixels trajectories). I demo this tool in this video for the 2021 UCL Neuropixels course.These functions aren't maintainted for general use but may be useful:
Neuropixels raster viewer A viewer for Neuropixels data as rasters (aligned to events, grouped, sorted, single/multiunit).
Widefield deconvolution (GCaMP6s) Deconvolve fluorescence from widefield GCaMP6s imaging (also requires kernel saved into same folder as code). Kernel was made from simultaneous cortical widefield imaging and electrophysiology in Peters et al., Nature 2021.
Bi/tri-color colormaps Bi/tricolor colormaps that interpolate luminance in CIELAB space and can specify gamma value.