def inhibitory_astro_queries(mouse_number):
"""The query format expanded to include astrocytes for 2ss
"""
listOfQueries = []
punctum_size = 2
for slice_span in range(1, 4):
# Query 3
preIF_str1 = str(mouse_number) + 'ss_Synap.tif'
preIF_str2 = str(mouse_number) + 'ss_GAD.tif'
preIF = [preIF_str1, preIF_str2]
preIF_z = [slice_span, slice_span]
postIF_str1 = str(mouse_number) + 'ss_Geph.tif'
postIF = [postIF_str1]
postIF_z = [slice_span]
glialIF_str = str(mouse_number) + 'ss_GS.tif'
glialIF = [glialIF_str]
glialIF_z = [slice_span]
query = {
'glialIF': glialIF,
'glialIF_z': glialIF_z,
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
data = {'listOfQueries': listOfQueries}
fn = '/Users/anish/Documents/Connectome/SynapseAnalysis/data/fragile_x/queries/' + \
str(mouse_number) + 'ss_inhibitory_astro_queries.json'
da.writeJSONFile(fn, data)
def main():
# The 2D Blob size xy, units: pixels
punctumSize = 2
# Threshold associated with query (optional)
thresh = 0.7
listOfQueries = []
## QUERY 1
preIF = ['synapsin_1st.tif'] #corresponds to the file name
preIF_z = [2]
postIF = ['PSD95m_1st.tif']
postIF_z = [2]
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctumSize,
'thresh': thresh
}
listOfQueries.append(query)
data = {'listOfQueries': listOfQueries}
fn = 'example_queries.json'
da.writeJSONFile(fn, data)
# Load Query File
querylist = syn.loadQueriesJSON(fn)
print(len(querylist))
def inhibitory_queries(mouse_number):
""" Inhibitory queries at different sizes
Parameters
-------------
mouse_number
"""
listOfQueries = []
punctum_size = 2
for slice_span in range(1, 4):
# Query - 1
preIF_str1 = str(mouse_number) + 'ss_Synap.tif'
preIF_str2 = str(mouse_number) + 'ss_GAD.tif'
preIF = [preIF_str1, preIF_str2]
preIF_z = [slice_span, slice_span]
postIF_str1 = str(mouse_number) + 'ss_Geph.tif'
postIF = [postIF_str1]
postIF_z = [slice_span]
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
data = {'listOfQueries': listOfQueries}
fn = '/Users/anish/Documents/Connectome/SynapseAnalysis/data/fragile_x/queries/' + \
str(mouse_number) + 'ss_inhibitory_queries.json'
da.writeJSONFile(fn, data)
def excitatory_ratio_test2(mouse_number):
""" List of excitatory queries
Parameters
-------------
mouse_number
"""
listOfQueries = []
punctum_size = 2
# Query 0
preIF_str = str(mouse_number) + 'ss_Synap.tif'
preIF = [preIF_str]
preIF_z = [1]
postIF_str = str(mouse_number) + 'ss_PSD.tif'
postIF = [postIF_str]
postIF_z = [2]
query = {'preIF': preIF, 'preIF_z': preIF_z, 'postIF': postIF,
'postIF_z': postIF_z, 'punctumSize': punctum_size}
listOfQueries.append(query)
# Query 1
preIF_str1 = str(mouse_number) + 'ss_Synap.tif'
preIF_str2 = str(mouse_number) + 'ss_VGluT1.tif'
preIF = [preIF_str1, preIF_str2]
preIF_z = [2, 2]
postIF_str = str(mouse_number) + 'ss_PSD.tif'
postIF = [postIF_str]
postIF_z = [1]
query = {'preIF': preIF, 'preIF_z': preIF_z, 'postIF': postIF,
'postIF_z': postIF_z, 'punctumSize': punctum_size}
listOfQueries.append(query)
# Query 2
preIF_str1 = str(mouse_number) + 'ss_Synap.tif'
preIF_str2 = str(mouse_number) + 'ss_VGluT2.tif'
preIF = [preIF_str1, preIF_str2]
preIF_z = [2, 2]
postIF_str = str(mouse_number) + 'ss_PSD.tif'
postIF = [postIF_str]
postIF_z = [1]
query = {'preIF': preIF, 'preIF_z': preIF_z, 'postIF': postIF,
'postIF_z': postIF_z, 'punctumSize': punctum_size}
listOfQueries.append(query)
data = {'listOfQueries': listOfQueries}
fn = '/Users/anish/Documents/Connectome/SynapseAnalysis/data/fragile_x/queries/' + \
str(mouse_number) + 'ss_ratio2_queries.json'
da.writeJSONFile(fn, data)
def single_channel_queries(mouse_number):
""" Single channel queries
Parameters
-------------
mouse_number
"""
listOfQueries = []
punctum_size = 2
for slice_span in range(1, 4):
# Query 0 - PSD-95
preIF = []
preIF_z = []
postIF_str = str(mouse_number) + 'ss_PSD.tif'
postIF = [postIF_str]
postIF_z = [slice_span]
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
# Query 1 - Synapsin
preIF_str1 = str(mouse_number) + 'ss_Synap.tif'
preIF = [preIF_str1]
preIF_z = [slice_span]
postIF = []
postIF_z = []
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
# Query 2 - VGluT1
preIF_str1 = str(mouse_number) + 'ss_VGluT1.tif'
preIF = [preIF_str1]
preIF_z = [slice_span]
postIF = []
postIF_z = []
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
# Query 3 - VGluT2
preIF_str1 = str(mouse_number) + 'ss_VGluT2.tif'
preIF = [preIF_str1]
preIF_z = [slice_span]
postIF = []
postIF_z = []
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
# Query 4 - Gephyrin
preIF = []
preIF_z = []
postIF_str = str(mouse_number) + 'ss_Geph.tif'
postIF = [postIF_str]
postIF_z = [slice_span]
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
# Query 5 - GAD
preIF_str1 = str(mouse_number) + 'ss_GAD.tif'
preIF = [preIF_str1]
preIF_z = [slice_span]
postIF = []
postIF_z = []
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
# Query 6 - GS
preIF_str1 = str(mouse_number) + 'ss_GS.tif'
preIF = [preIF_str1]
preIF_z = [slice_span]
postIF = []
postIF_z = []
query = {
'preIF': preIF,
'preIF_z': preIF_z,
'postIF': postIF,
'postIF_z': postIF_z,
'punctumSize': punctum_size
}
listOfQueries.append(query)
data = {'listOfQueries': listOfQueries}
fn = '/Users/anish/Documents/Connectome/SynapseAnalysis/data/fragile_x/queries/' + \
str(mouse_number) + 'ss_puncta_queries.json'
da.writeJSONFile(fn, data)
