log_pd, store, cb, data_c, mode_bleach_detection, frap_start_delay)
log_pd = pd.concat([log_pd, coordinate_pd], axis=1)
# link pointer with corresponding organelle
log_pd['%s' % analyze_organelle] = obj.points_in_objects(
label_organelle, log_pd['x'], log_pd['y'])
# calculate distance to organelle boundary
_, distance_map = medial_axis(organelle, return_distance=True)
distance_lst = []
for i in range(len(log_pd)):
distance_lst.append(distance_map[log_pd['y'][i]][log_pd['x'][i]])
log_pd['distance'] = distance_lst
# generate bleach spot mask and bleach spots dataframe (pointer_pd)
bleach_spots, pointer_pd = ble.get_bleach_spots(
log_pd, label_organelle, analyze_organelle, num_dilation)
data_log['num_bleach_spots'] = [obj.object_count(bleach_spots)]
print("%d spots passed filters for analysis." %
data_log['num_bleach_spots'][0])
# add bleach spots corresponding organelle measurements
pointer_pd = dat.copy_based_on_index(
pointer_pd, organelle_pd, '%s' % analyze_organelle,
'%s' % analyze_organelle, [
'%s_x' % analyze_organelle,
'%s_y' % analyze_organelle,
'%s_size' % analyze_organelle,
'%s_mean_int' % analyze_organelle,
'%s_circ' % analyze_organelle
], ['x', 'y', 'size', 'raw_int', 'circ'])
# get bleach_frame
log_pd['bleach_frame'] = dat.get_frame(log_pd['time'], acquire_time_tseries)
# get bleach spot coordinate
coordinate_pd = ble.get_bleach_spots_coordinates(log_pd, store, cb, data_c,
mode_bleach_detection,
frap_start_delay)
log_pd = pd.concat([log_pd, coordinate_pd], axis=1)
# link pointer with corresponding nucleoli
log_pd['nucleoli'] = obj.points_in_objects(label_nucleoli, log_pd['x'],
log_pd['y'])
# generate bleach spot mask and bleach spots dataframe (pointer_pd)
bleach_spots, pointer_pd = ble.get_bleach_spots(log_pd, label_nucleoli,
num_dilation)
data_log['num_bleach_spots'] = [obj.object_count(bleach_spots)]
print("%d spots passed filters for analysis." %
data_log['num_bleach_spots'][0])
# add bleach spots corresponding nucleoli measurements
pointer_pd = dat.copy_based_on_index(
pointer_pd, nucleoli_pd, 'nucleoli', 'nucleoli', [
'nucleoli_x', 'nucleoli_y', 'nucleoli_size', 'nucleoli_mean_int',
'nucleoli_circ'
], ['x', 'y', 'size', 'raw_int', 'circ'])
# --------------------------------------------------
# FRAP CURVE ANALYSIS from bleach spots
# --------------------------------------------------
print("### Image analysis: FRAP curve calculation ...")