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)