nickponvert

# @nickponvert
# Code for hierarchical bootstrapping

class HData():
    def __init__(self, df, hierarchy, random_effect=None):
        '''
        A tree-structured representation of a DataFrame with hierarchical structure. 
        Can be resampled while respecting the hierarchy, allowing for bootstrap statistics that 
        take the structure of the data into account. Inspired by Saravanan et al. 2019
        https://www.biorxiv.org/content/10.1101/819334v1.full.pdf+html

nickponvert

import h5py
import datetime
import pandas as pd
import numpy as np
import ast  # To parse string representing a list

def save_hdf(dframe, filename):
    '''
    Save dataframe as HDF5, in a cleaner format than pandas.DataFrame.to_hdf()
    Use load_hdf() to load these files.

nickponvert

from jaratoolbox import loadopenephys
#from jaratoolbox import spikesanalysis
import numpy as np
import matplotlib.pyplot as plt
import os


class Aligned_Spikes():

    def __init__(self, directory, tetrode_number):

nickponvert

from pylab import *
from jaratoolbox import loadopenephys

import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import numpy as np



# -- Load the required data --

nickponvert

nickponvert

Cryopreservation, mounting and sectioning

Postfix specimen in PAF in phosphate buffer

Wash in fix buffer - .1 M phosphate buffer 3 times for 5 minutes each wash

Melt an aliquot of agar-sucrose solution (1.5% agar, 5% sucrose) and let cool to 40C

Immerse brain in agar inside mold and let cool until solidified (5-10 mins)

nickponvert

update_current_git_vars