def synapsin_pairwise():
"""
Synapsin Pairwise
Return
-----------
list_of_df : dataframe list
"""
list_of_df = []
base_dir = '/Users/anish/Documents/Connectome/Synaptome-Duke/data/antibodyanalysis/pairwise/KDM-SYN-090210/Synapsin/'
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
target_antibody_name1 = 'synapsinGP1stA.tif'
target_antibody_name2 = 'synapsinR1stA.tif'
# QUERY 1
query1 = {
'preIF': ['synapsinGP1stA.tif'],
'preIF_z': [1],
'postIF': ['psd1stA.tif'],
'postIF_z': [1],
'punctumSize': 2
}
query2 = {
'preIF': ['synapsinR1stA.tif'],
'preIF_z': [1],
'postIF': ['psd1stA.tif'],
'postIF_z': [1],
'punctumSize': 2
}
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('Synapsin dataframe: ')
print(df)
# QUERY 2
query1['preIF_z'] = [2]
query1['postIF_z'] = [1]
query2['preIF_z'] = [2]
query2['postIF_z'] = [1]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('Synapsin dataframe: ')
print(df)
# QUERY 3
query1['preIF_z'] = [2]
query1['postIF_z'] = [2]
query2['preIF_z'] = [2]
query2['postIF_z'] = [2]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('Synapsin dataframe: ')
print(df)
# QUERY 4
query1['preIF_z'] = [3]
query1['postIF_z'] = [1]
query2['preIF_z'] = [3]
query2['postIF_z'] = [1]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('Synapsin dataframe: ')
print(df)
return list_of_df
def cav31_pairwise():
"""
CAV31 pairwise comparison
Return
---------
list_of_df : dataframe list
"""
list_of_df = []
base_dir = '/Users/anish/Documents/Connectome/Synaptome-Duke/data/antibodyanalysis/pairwise/KDM-MH-131023/Cav3.1/'
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
target_antibody_name1 = 'Cav31M_1st_A.tif'
target_antibody_name2 = 'Cav31R_1st_A.tif'
# QUERY 1
query1 = {
'preIF': ['VGluT1_1st_A.tif'],
'preIF_z': [1],
'postIF': ['Cav31M_1st_A.tif'],
'postIF_z': [1],
'punctumSize': 2
}
query2 = {
'preIF': ['VGluT1_1st_A.tif'],
'preIF_z': [1],
'postIF': ['Cav31R_1st_A.tif'],
'postIF_z': [1],
'punctumSize': 2
}
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('CAV31 dataframe: ')
print(df)
# QUERY 2
query1['preIF_z'] = [1]
query1['postIF_z'] = [2]
query2['preIF_z'] = [1]
query2['postIF_z'] = [2]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('CAV31 dataframe: ')
print(df)
# QUERY 3
query1['preIF_z'] = [2]
query1['postIF_z'] = [2]
query2['preIF_z'] = [2]
query2['postIF_z'] = [2]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('CAV31 dataframe: ')
print(df)
# QUERY 4
query1['preIF_z'] = [1]
query1['postIF_z'] = [3]
query2['preIF_z'] = [1]
query2['postIF_z'] = [3]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('CAV31 dataframe: ')
print(df)
return list_of_df
def psd95_pairwise():
"""
PSD95 pairwise comparisons
Parameters
-------------
None
Return
-------------
list_of_df : dataframe list
"""
list_of_df = []
base_dir = '/Users/anish/Documents/Connectome/Synaptome-Duke/data/antibodyanalysis/pairwise/KDM-RW-120419/'
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
target_antibody_name1 = 'PSD95m_1st.tif'
target_antibody_name2 = 'PSD95r_2nd.tif'
# QUERY 1
query1 = {
'preIF': ['synapsin_1st.tif'],
'preIF_z': [1],
'postIF': ['PSD95m_1st.tif'],
'postIF_z': [1],
'punctumSize': 2
}
query2 = {
'preIF': ['synapsin_1st.tif'],
'preIF_z': [1],
'postIF': ['PSD95r_2nd.tif'],
'postIF_z': [1],
'punctumSize': 2
}
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('PSD-95 dataframe: ')
print(df)
# QUERY 2
query1['preIF_z'] = [1]
query1['postIF_z'] = [2]
query2['preIF_z'] = [1]
query2['postIF_z'] = [2]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('PSD-95 dataframe: ')
print(df)
# QUERY 3
query1['preIF_z'] = [2]
query1['postIF_z'] = [2]
query2['preIF_z'] = [2]
query2['postIF_z'] = [2]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('PSD-95 dataframe: ')
print(df)
# QUERY 4
query1['preIF_z'] = [1]
query1['postIF_z'] = [3]
query2['preIF_z'] = [1]
query2['postIF_z'] = [3]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('PSD-95 dataframe: ')
print(df)
return list_of_df
def vglut1_pairwise():
"""
VGLUT1 pairwise comparison
Return
----------
list_of_df : dataframe list
"""
list_of_df = []
base_dir = '/Users/anish/Documents/Connectome/Synaptome-Duke/data/antibodyanalysis/pairwise/KDM-SYN-090210/VGluT1/'
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
target_antibody_name1 = 'VGlut1GP1stA.tif'
target_antibody_name2 = 'VGlut1M1stA.tif'
query1 = {
'preIF': ['VGlut1GP1stA.tif', 'synapsin1stA.tif'],
'preIF_z': [1, 1],
'postIF': [],
'postIF_z': [],
'punctumSize': 2
}
query2 = {
'preIF': ['VGlut1M1stA.tif', 'synapsin1stA.tif'],
'preIF_z': [1, 1],
'postIF': [],
'postIF_z': [],
'punctumSize': 2
}
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('VGLUT1 dataframe: ')
print(df)
# QUERY 2
query1['preIF_z'] = [2, 1]
query2['preIF_z'] = [2, 1]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('VGLUT1 dataframe: ')
print(df)
# QUERY 3
query1['preIF_z'] = [2, 2]
query2['preIF_z'] = [2, 2]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('VGLUT1 dataframe: ')
print(df)
# QUERY 4
query1['preIF_z'] = [3, 1]
query2['preIF_z'] = [3, 1]
measure_list = aa.run_pairwise(query1, query2, target_antibody_name1,
target_antibody_name2, base_dir, thresh,
resolution)
df = aa.create_pairwise_df(measure_list[0], measure_list[1],
target_antibody_name1, target_antibody_name2)
list_of_df.append(df)
print('VGLUT1 dataframe: ')
print(df)
return list_of_df