detect_puffs is a plugin for the image processing program flika. It contains a set of algorithms for detecting local calcium signals from movies.
How to detect subcellular Ca2+ signals using flika
Guide to setting threshold_cluster() parameters
from plugins.detect_puffs.threshold_cluster import threshold_cluster
from plugins.detect_puffs.puff_simulator.puff_simulator import simulate_puffs
simulate_puffs(nFrames=1000,nPuffs=20)
baseline = -5 # This is the mean pixel value in the absence of photons.
subtract(baseline)
data_window=ratio(0, 30, 'average') # ratio(first_frame, nFrames, ratio_type). Now we are in F/F0
data_window.setName('Data Window (F/F0)')
norm_image = data_window.image - 1
norm_window = Window(norm_image)
norm_window.setName('Normalized Window')
blurred_window = gaussian_blur(2, norm_edges=True, keepSourceWindow=True)
blurred_window.setName('Blurred Window')
threshold_cluster(data_window, blurred_window, blurred_window, blur_thresh=.1)