def iterate_over_queries():
channel_name = 'ss_PSD.tif'
query_number = 4
df_list = iterate_over_mice(query_number, channel_name)
aa.write_dfs_to_excel(df_list, 'blob_synapse', 'psd_q4_ratio.xlsx')
channel_name = 'ss_VGluT1.tif'
query_number = 5
df_list = iterate_over_mice(query_number, channel_name)
aa.write_dfs_to_excel(df_list, 'blob_synapse', 'vglut1_q5_ratio.xlsx')
channel_name = 'ss_Synap.tif'
query_number = 5
df_list = iterate_over_mice(query_number, channel_name)
aa.write_dfs_to_excel(df_list, 'blob_synapse', 'synap_q5_ratio.xlsx')
channel_name = 'ss_VGluT2.tif'
query_number = 6
df_list = iterate_over_mice(query_number, channel_name)
aa.write_dfs_to_excel(df_list, 'blob_synapse', 'vglut2_q6_ratio.xlsx')
channel_name = 'ss_Synap.tif'
query_number = 6
df_list = iterate_over_mice(query_number, channel_name)
aa.write_dfs_to_excel(df_list, 'blob_synapse', 'synap_q6_ratio.xlsx')
def main():
""" Run comparisons """
VGLUT3_df = VGLUT3()
sheet_name = '20180424_AT_VGLUT3'
fn = '20180424_AT_VGLUT3.xlsx'
df_list = [VGLUT3_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
CPU_df = CPU()
sheet_name = '20180417_AT_CPU'
fn = '20180417_AT_CPU.xlsx'
df_list = [CPU_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
COMP_df = COMP()
sheet_name = '20180727_Microscope_TBS_NM'
fn = '20180727_Microscope_TBS_NM.xlsx'
df_list = [COMP_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
NM_Scope_df = NM_Scope()
sheet_name = 'NM_Scope'
fn = 'NM_Scope.xlsx'
df_list = [NM_Scope_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
SAPAP3_df = SAPAP3()
sheet_name = '20180320_AT_SAPAP3'
fn = '20180320_AT_SAPAP3.xlsx'
df_list = [SAPAP3_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main(): #Do not change
""" Run comparisons """
NAME_df = Name() #The "NAME" should match the term used in line 13
sheet_name = 'YYYYMMDD_(project title)' #name of excel sheet
fn = 'YYYMMDD_(project title).xlsx' #name of excel file
df_list = [NAME_df] # the term inside the brackets must match the _____df in line 155
aa.write_dfs_to_excel(df_list, sheet_name, fn) #Do not change
def main():
""" Run comparisons """
N452_df = N452()
sheet_name = '20180202_AT_N452'
fn = '20180202_AT_N452.xlsx'
df_list = [N452_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run homer comparisons """
homer_df = homer()
sheet_name = 'Homer-L113'
fn = 'Homer-L113.xlsx'
df_list = [homer_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
VMAT2_df = VMAT2()
sheet_name = '20180627_N449_VMAT2_Parent'
fn = '20180627_N449_VMAT2_Parent.xlsx'
df_list = [VMAT2_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
VIP_df = VIP()
sheet_name = '20180316_AT_VIP'
fn = '20180316_AT_VIP.xlsx'
df_list = [VIP_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
GABRA4_df = GABRA4()
sheet_name = '20180524_N398A_GABRA4'
fn = '20180524_N398A_GABRA4.xlsx'
df_list = [GABRA4_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
BASSOON_df = BASSOON()
sheet_name = '20180607_L124_Isotype'
fn = '20180607_L124_Isotype.xlsx'
df_list = [BASSOON_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
N39B_df = N39B()
sheet_name = '20180609_N39_N416_N59'
fn = '220180609_N39_N416_N59.xlsx'
df_list = [N39B_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
SYN3_df = SYN3()
sheet_name = '20180124_AT_SYN3_Hip'
fn = '20180124_AT_SYN3_Hip.xlsx'
df_list = [SYN3_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
cck_df = cask()
sheet_name = 'cask-K56A'
fn = 'cask-K56A-1,2.xlsx'
df_list = [cck_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
ISOTYPE_df = ISOTYPE()
sheet_name = '20180620_L106_ISOTYPE'
fn = '20180620_L106_ISOTYPE.xlsx'
df_list = [ISOTYPE_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
validation_df = validation()
sheet_name = 'validation-cortex-6'
fn = 'validation-cortex-6.xlsx'
df_list = [validation_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
SHANK1_df = SHANK1()
sheet_name = '20180216_AT_SHANK1'
fn = '20180216_AT_SHANK1.xlsx'
df_list = [SHANK1_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run comparisons """
MULTI_df = MULTI()
sheet_name = '20180516_N39B_N50_N422_N23B'
fn = '20180516_N39B_N50_N422_N23B.xlsx'
df_list = [MULTI_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run homer comparisons """
mitochrondia_170906_df = mitochrondia_170906()
sheet_name = 'mitochrondia_170906'
fn = 'mitochrondia_170906.xlsx'
df_list = [mitochrondia_170906_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run homer comparisons """
isotype_specific_df = isotype_specific()
sheet_name = 'isotype_specific'
fn = 'isotype_specific.xlsx'
df_list = [isotype_specific_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
"""Run pairwise comparisons and save to an excel file"""
cav31_dflist = cav31_pairwise()
gephyrin_dflist = gephyrin_pairwise()
synapsin_dflist = synapsin_pairwise()
psd_dflist = psd95_pairwise()
vglut1_dflist = vglut1_pairwise()
sheet_name = 'Pairwise'
fn = 'pairwise_comparisons2.xlsx'
df_list = synapsin_dflist + vglut1_dflist + psd_dflist + gephyrin_dflist + cav31_dflist
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run concentration comparisons """
synapsin_df = synapsin_concentrations()
glur1_df = glur1_concentrations()
glur2_df = glur2_concentrations()
glur3_df = glur3_concentrations()
nr1_df = nr1_concentrations()
sheet_name = 'Concentration'
fn = 'concentration_comparisons.xlsx'
df_list = [synapsin_df, glur1_df, glur2_df, glur3_df, nr1_df]
#df_list = [nr1_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
"""Run pairwise comparisons and save to an excel file"""
gephyrin_df = gephyrin_pairwise()
cav31_df = cav31_pairwise()
synapsin_df = synapsin_pairwise()
psd_df = psd95_pairwise()
vglut1_df = vglut1_pairwise()
sheet_name = 'Pairwise'
fn = 'pairwise_comparisons.xlsx'
df_list = [synapsin_df, vglut1_df, psd_df, gephyrin_df, cav31_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
# Output filename
fn = 'sact_psd_example.xlsx'
sheet_name = 'sact_psd_example'
# Determine if file exists. This is only an issue when running on windows
if os.path.isfile(fn):
print('A sheet with this name already exists; rename sheet and rerun')
if socket.gethostname() != 'anish': #this line is optional
sys.exit()
psd_df = psd_pairwise_comparison()
df_list = [psd_df]
# Export the dataframe to excel
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def main():
""" Run concentration comparisons """
bassoon_psd_21_df = bassoon_L170921_psd_multipleclones()
bassoon_vglut1_21_df = bassoon_L170921_vglut1_multipleclones()
bassoon_20 = bassoon_L170920_multipleclones()
irsp53_df = irsp53_lowicryl_multipleclones()
homer_df = homer_multipleclones()
vgat_df = VGAT_LRWhite_multipleclones()
collybistin_df = collybistin_multipleclones()
gephyrin_df = gephyrin_multipleclones()
irsp53_3_df = irsp53_lowicryl_multipleclones3()
basson_3_21_df = bassoon_L170921_multipleclones3()
sheet_name = 'Multipleclones'
fn = 'multipleclones.xlsx'
df_list = [gephyrin_df, homer_df, irsp53_df, vgat_df, collybistin_df,
bassoon_20, bassoon_vglut1_21_df, bassoon_psd_21_df, basson_3_21_df, irsp53_3_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
def write_df(vol_name_list, signal_list, output_fn):
"""Save signal measurement results as a df
Paramters
---------------
vol_name_list : list of strs
signal_list : list of floats
output_fn : str - output filename
Return
----------------
df : dataframe
"""
column_labels = ['YFP Size']
df = pd.DataFrame(np.nan, index=vol_name_list, columns=column_labels)
df.iloc[:, 0] = signal_list
sheet_name = 'YFP Size'
df_list = [df]
aa.write_dfs_to_excel(df_list, sheet_name, output_fn)
return df
def run_list_of_queries(mouse_number, mouse_project_str, sheet_name):
"""
run queries in a parallel manner
Parameters
-----------------
mouse_number : int
mouse_project_str : str
sheet_name : str
"""
output_foldername = 'results_' + sheet_name
query_fn = 'queries/' + mouse_project_str + '_queries.json'
data_location = '/Users/anish/Documents/yi_mice/' + \
str(mouse_number) + 'ss_stacks/'
hostname = socket.gethostname()
if hostname == 'Galicia':
data_location = '/data5TB/yi_mice/' + str(mouse_number) + 'ss_stacks'
dapi_mask_str_base = '/data5TB/yi_mice/dapi-masks/' + \
str(mouse_number) + 'ss_stacks'
print('Query Filename: ', query_fn)
print('Data Location: ', data_location)
print('OutputFoldername: ', output_foldername)
print('Sheetname: ', sheet_name)
listOfQueries = syn.loadQueriesJSON(query_fn)
resolution = {'res_xy_nm': 100, 'res_z_nm': 70}
region_name_base = 'F00'
thresh = 0.9
result_list = []
num_workers = mp.cpu_count() - 1
print(num_workers)
pool = mp.Pool(num_workers)
atet_inputs_list = []
mask_location_str = -1
queryID = 0
foldernames = []
for region_num in range(0, 4):
region_name = region_name_base + str(region_num)
data_region_location = os.path.join(data_location, region_name)
dapi_mask_str = os.path.join(dapi_mask_str_base, region_name)
for nQuery, query in enumerate(listOfQueries):
foldername = region_name + '-Q' + str(nQuery)
foldernames.append(foldername)
print(foldername)
mask_location_str = -1
#dapi_mask_str = -1
atet_input = {
'query': query,
'queryID': queryID,
'nQuery': nQuery,
'resolution': resolution,
'data_region_location': data_region_location,
'data_location': data_location,
'output_foldername': output_foldername,
'region_name': region_name,
'mask_str': mask_location_str,
'dapi_mask_str': dapi_mask_str,
'mouse_number': mouse_number
}
atet_inputs_list.append(atet_input)
queryID = queryID + 1
# Run processes
result_list = pool.map(sa.run_synapse_detection, atet_inputs_list)
pool.close()
pool.join()
print('Get process results from the output queue')
sorted_queryresult = sa.organize_result_lists(result_list)
mouse_df = sa.create_synapse_df(sorted_queryresult, foldernames)
print(mouse_df)
fn = sheet_name + '.xlsx'
df_list = [mouse_df]
aa.write_dfs_to_excel(df_list, sheet_name, fn)
