In [1]:
%load_ext autoreload
%autoreload 2
In [2]:
import os
import expipe
import pathlib
import numpy as np
import spatial_maps.stats as stats
import septum_mec
import septum_mec.analysis.data_processing as dp
import septum_mec.analysis.registration
import head_direction.head as head
import spatial_maps as sp
import speed_cells.speed as spd
import re
import joblib
import multiprocessing
import shutil
import psutil
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib
# import seaborn as sns
from distutils.dir_util import copy_tree
from neo import SpikeTrain
import scipy

from tqdm.notebook import tqdm_notebook as tqdm
tqdm.pandas()

from spike_statistics.core import permutation_resampling

from spikewaveform.core import calculate_waveform_features_from_template, cluster_waveform_features

from septum_mec.analysis.plotting import violinplot, despine

13:30:10 [I] klustakwik KlustaKwik2 version 0.2.6
In [29]:
%matplotlib inline
plt.rc('axes', titlesize=12)
plt.rcParams.update({
    'font.size': 12, 
    'figure.figsize': (6, 4), 
    'figure.dpi': 150
})

output_path = pathlib.Path("output") / "cell-count"
(output_path / "statistics").mkdir(exist_ok=True, parents=True)
(output_path / "figures").mkdir(exist_ok=True, parents=True)
output_path.mkdir(exist_ok=True)
In [4]:
data_loader = dp.Data()
actions = data_loader.actions
project = data_loader.project
In [5]:
identification_action = actions['identify-neurons']
sessions = pd.read_csv(identification_action.data_path('sessions'))
units = pd.read_csv(identification_action.data_path('units'))
session_units = pd.merge(sessions, units, on='action')
In [6]:
stim_action = actions['stimulus-response']
stim_results = pd.read_csv(stim_action.data_path('results'))
In [8]:
statistics_action = actions['calculate-statistics']
shuffling = actions['shuffling']

statistics_results = pd.read_csv(statistics_action.data_path('results'))
statistics_results = session_units.merge(statistics_results, how='left')
quantiles_95 = pd.read_csv(shuffling.data_path('quantiles_95'))
action_columns = ['action', 'channel_group', 'unit_name']
data = pd.merge(statistics_results, quantiles_95, on=action_columns, suffixes=("", "_threshold"))
In [9]:
data['unit_day'] = data.apply(lambda x: str(x.unit_idnum) + '_' + x.action.split('-')[1], axis=1)
In [10]:
data = data.merge(stim_results, how='left')
In [11]:
waveform_action = actions['waveform-analysis']
waveform_results = pd.read_csv(waveform_action.data_path('results')).drop('template', axis=1)
In [12]:
data = data.merge(waveform_results, how='left')
In [13]:
colors = ['#d95f02','#e7298a']
labels = ['11 Hz', '30 HZ']
queries = ['frequency==11', 'frequency==30']
In [14]:
data.bs = data.bs.astype(bool)
In [15]:
data.loc[data.eval('t_i_peak == t_i_peak and not bs'), 'ns_inhibited'] = True
data.ns_inhibited.fillna(False, inplace=True)

data.loc[data.eval('t_i_peak != t_i_peak and not bs'), 'ns_not_inhibited'] = True
data.ns_not_inhibited.fillna(False, inplace=True)
In [16]:
query = (
    'gridness > gridness_threshold and '
    'information_rate > information_rate_threshold and '
    'gridness > .2 and '
    'average_rate < 25'
)
sessions_above_threshold = data.query(query)
print("Number of sessions above threshold", len(sessions_above_threshold))
print("Number of animals", len(sessions_above_threshold.groupby(['entity'])))

Number of sessions above threshold 194
Number of animals 4
In [17]:
gridcell_sessions = data[data.unit_day.isin(sessions_above_threshold.unit_day.values)]
print("Number of gridcells", gridcell_sessions.unit_idnum.nunique())
print("Number of gridcell recordings", len(gridcell_sessions))
print("Number of animals", len(gridcell_sessions.groupby(['entity'])))

Number of gridcells 139
Number of gridcell recordings 231
Number of animals 4
In [18]:
data.loc[:,'gridcell'] = np.nan
data['gridcell'] = data.isin(gridcell_sessions)

data.loc[data.eval('not gridcell and bs'), 'bs_not_gridcell'] = True
data.bs_not_gridcell.fillna(False, inplace=True)
In [28]:
table = pd.DataFrame()
table['Gridcell'] = data.drop_duplicates('unit_idnum').query('gridcell').groupby('entity')['action'].count()
table['BS not gridcell'] = data.drop_duplicates('unit_idnum').query('bs_not_gridcell').groupby('entity')['action'].count()
table['NSi'] = data.drop_duplicates('unit_idnum').query('ns_inhibited').groupby('entity')['action'].count()
table['NSni'] = data.drop_duplicates('unit_idnum').query('ns_not_inhibited').groupby('entity')['action'].count()
table
Out[28]:
Gridcell BS not gridcell NSi NSni
entity
1833 94 165 16 52
1834 14 216 4 7
1839 19 70 11 5
1849 8 229 8 23
In [ ]:

Store results in Expipe action

In [35]:
action = project.require_action("cell-count")
In [36]:
copy_tree(output_path, str(action.data_path()))
Out[36]:
['/media/storage/expipe/septum-mec/actions/stimulus-response/data/data/times.feather',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/data/psth.feather',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-bs_not_gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_not_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-bs_not_gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-nsi-ns.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-nsi-ns-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_not_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_not_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_not_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_not_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_not_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-bs_not_gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-bs_not_gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-bs_not_gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-bs_not_gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_not_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-nsi-ns-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-bs_not_gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-bs_not_gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-gc-ns.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-bs_not_gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_not_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_not_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-nsi-ns.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-gc-ns-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-gc-ns.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_not_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_not_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-bs_not_gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-bs_not_gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-bs_not_gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-bs_not_gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/response-probability-gc-ns-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-bs_not_gridcell.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_not_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_not_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-bs_not_gridcell-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_not_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_inhibited-stim-mec.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-gridcell.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_e_peak-ns_not_inhibited.svg',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-bs_not_gridcell-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_e_peak-ns_not_inhibited.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-p_i_peak-ns_inhibited-stim-mec.png',
 '/media/storage/expipe/septum-mec/actions/stimulus-response/data/figures/histogram-t_i_peak-ns_inhibited.png']
In [37]:
septum_mec.analysis.registration.store_notebook(action, "20_cell_count.ipynb")
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In [ ]: