def VGAT_lowicryl_multipleclones():
""" VGAT_lowicryl_multipleclones
"""
base_dir = '/Users/anish/Documents/Connectome/Synaptome-Duke/data/antibodyanalysis/L118-VGAT/Lowicryl/'
folder_names = aa.getListOfFolders(base_dir)
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
conjugate_filename_str = 'GAD'
target_filename_str = 'VGAT'
conjugate_filenames = []
target_filenames = []
query_list = []
for foldername in folder_names:
target_name = aa.find_filename(target_filename_str, foldername, base_dir)
conjugate_name = aa.find_filename(conjugate_filename_str, foldername, base_dir)
conjugate_filenames.append(conjugate_name)
target_filenames.append(target_name)
query = {'preIF': [target_name, conjugate_name], 'preIF_z': [2, 2],
'postIF': [], 'postIF_z': [],
'punctumSize': 2}
query_list.append(query)
measure_list = aa.calculate_measure_lists(query_list, folder_names, base_dir,
thresh, resolution, target_filenames)
df = aa.create_df(measure_list, folder_names, target_filenames, conjugate_filenames)
print(df)
return df
def mitochrondia_170906():
""" Run antibody characterization tool on the L113-Homer dataset
Return
----------
df : dataframe - contains results
"""
# Location of data
base_dir = '/Users/anish/Dropbox/KDM-SYN-170906/'
folder_names = aa.getListOfFolders(base_dir)
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
conjugate_filename_str = 'VDAC'
target_filename_str = 'N152'
conjugate_filenames = []
target_filenames = []
query_list = []
for foldername in folder_names:
target_name = aa.find_filename(target_filename_str, foldername, base_dir)
conjugate_name = aa.find_filename(conjugate_filename_str, foldername, base_dir)
conjugate_filenames.append(conjugate_name)
target_filenames.append(target_name)
query = {'preIF': [], 'preIF_z': [],
'postIF': [target_name, conjugate_name], 'postIF_z': [2, 2],
'punctumSize': 2}
query_list.append(query)
measure_list = aa.calculate_measure_lists(query_list, folder_names, base_dir,
thresh, resolution, target_filenames)
df = aa.create_df(measure_list, folder_names, target_filenames, conjugate_filenames)
print(df)
return df
def bassoon_L170921_multipleclones3():
""" bassoon_L170921_multipleclones
"""
base_dir = '/Users/anish/Documents/Connectome/Synaptome-Duke/data/antibodyanalysis/L170921-Bassoon/'
folder_names = aa.getListOfFolders(base_dir)
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
thresh = 0.9
conjugate_filename_str = 'PSD'
conjugate_filename_str2 = 'VGluT1'
target_filename_str = 'L124'
conjugate_filenames = []
target_filenames = []
query_list = []
for foldername in folder_names:
target_name = aa.find_filename(target_filename_str, foldername, base_dir)
conjugate_name = aa.find_filename(conjugate_filename_str, foldername, base_dir)
conjugate_name2 = aa.find_filename(conjugate_filename_str2, foldername, base_dir)
conjugate_filenames.append(conjugate_name)
target_filenames.append(target_name)
query = {'preIF': [target_name, conjugate_name2], 'preIF_z': [1, 1],
'postIF': [conjugate_name], 'postIF_z': [1],
'punctumSize': 2}
query_list.append(query)
measure_list = aa.calculate_measure_lists(query_list, folder_names, base_dir,
thresh, resolution, target_filenames)
df = aa.create_df(measure_list, folder_names, target_filenames, conjugate_filenames)
print(df)
return df