Cortical Recording During Behavior

Analysis pipeline for cortical LFP recordings across behavioral contexts.

%load_ext autoreload
%autoreload 2

import logging
# Set logging to only show warnings and errors
logging.getLogger().setLevel(logging.WARNING)
import warnings

# Suppress specific warnings (e.g., RuntimeWarnings)
warnings.filterwarnings('ignore', category=RuntimeWarning)
%config InlineBackend.figure_format = 'svg'

from neurotools import nlab

import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns

# Create a 20 Hz sinusoidal signal
fs = 200  # Sampling frequency in Hz
t = np.arange(0, 10, 1/fs)  # 1 second time vector
freq = 2  # Frequency in Hz
sinusoid = np.sin(2 * np.pi * freq * t)

fig, ax = plt.subplots(figsize=(8, 3))
ax.plot(t, sinusoid)
ax.set_title('20 Hz Sinusoidal Signal')
ax.set_xlabel('Time (s)')
ax.set_ylabel('Amplitude')
ax.grid(True)
nlab.roundx(to=5)
nlab.hsigbar(1.1, 1.5, 0.8,dx=0.1,lw=1,color='red')

nlab.stderrplot(sinusoid, 0.1, color='blue', alpha=0.3)
plt.xlim(0, 1000)

ax= nlab.yscalebar(0.5, 0.2,'cat',x = 0.2, color='black')
nlab.addspikes(0.2,)
nlab.inhibition_arrow(0.1, 0.1,0.2,0.2, ax=ax, width=1,color='k')
nlab.figurebox(color='red')

nlab.boxplot

<function matplotlib.pyplot.boxplot(x: 'ArrayLike | Sequence[ArrayLike]', *, notch: 'bool | None' = None, sym: 'str | None' = None, vert: 'bool | None' = None, orientation: "Literal['vertical', 'horizontal']" = 'vertical', whis: 'float | tuple[float, float] | None' = None, positions: 'ArrayLike | None' = None, widths: 'float | ArrayLike | None' = None, patch_artist: 'bool | None' = None, bootstrap: 'int | None' = None, usermedians: 'ArrayLike | None' = None, conf_intervals: 'ArrayLike | None' = None, meanline: 'bool | None' = None, showmeans: 'bool | None' = None, showcaps: 'bool | None' = None, showbox: 'bool | None' = None, showfliers: 'bool | None' = None, boxprops: 'dict[str, Any] | None' = None, tick_labels: 'Sequence[str] | None' = None, flierprops: 'dict[str, Any] | None' = None, medianprops: 'dict[str, Any] | None' = None, meanprops: 'dict[str, Any] | None' = None, capprops: 'dict[str, Any] | None' = None, whiskerprops: 'dict[str, Any] | None' = None, manage_ticks: 'bool' = True, autorange: 'bool' = False, zorder: 'float | None' = None, capwidths: 'float | ArrayLike | None' = None, label: 'Sequence[str] | None' = None, data=None) -> 'dict[str, Any]'>