AP_scripts_peterslab

Scripts written after opening lab

NOTE: all functions are in +ap namespace, so are called as ap.function

Loading recordings

load_recording - calls:

• load_timelite/bonsai/mousecam/widefield/ephys, based on what's available and workspace structure load_parts
• parses wheel with ap.parse_wheel into wheel velocity and binary wheel_move vectors

Ephys

Preprocessing

• preprocess_neuropixels(animal,day) - saves metadata, runs PyKilosort, translates spike times into Open Ephys timestamps

Analysis

• spike_cg - auto/cross-correlation

Widefield

wf_align(im_unaligned,animal,day,align_type_master_align):

• create and save new day alignment: ap.align_widefield([],animal,[],'new_days') (uses all wf days, or specify im_unaligned/days for selection)

• create and save new animal alignment: ap.align_widefield(day-aligned retinotopy,animal,[],'new_animal') (aligns day-aligned average animal retinotopy to master retinotopy)

• wf_roi: grab fluorescence trace in ROI

• wf_draw: draw CCF borders/grid/point/areas over aligned widefield

• wf_reflect: flips L/R on aligned widefield image

• wf_load_raw: load/scroll raw frames

• wf_corrviewer: view seed pixel correlations in widefield

Data exploration

• expscroll - scroll through data

Plotting

• ccf_draw - draw CCF flat and 3D views, draw areas. plot probe trajectories
• plot_probe_positions - draw all probe positions (NTE and histology) for animal

Histology

• where2slice - show anterior/posterior extents of coronal slices from saved NTE trajectories