Find cells in all frames from a movie

find_cells.fiji.py

# This script runs on Fiji.
# Just drag and drop this file into a Fiji window.

from ij import IJ, ImageStack, ImagePlus
from ij.process import ImageProcessor
from ij.plugin import ImageCalculator, ZProjector
from ij.plugin.filter import GaussianBlur, Analyzer, ParticleAnalyzer
from ij.measure import Measurements
import sys


# Thresholding a movie (as ImagePlus)
def threshold(imp):
    threshold = 7
    sigma = 3

    # Subtract average of all frames from every frame
    proj = ZProjector(imp)
    proj.setMethod(ZProjector.AVG_METHOD)
    proj.doRGBProjection()
    imp_avg = proj.getProjection()
    imp_subt = ImageCalculator().run("Subtract create stack", imp, imp_avg)

    # Prepare a Gaussian blur filter
    blur = GaussianBlur()
    # Prepare ImageStack for result
    st = imp_subt.getImageStack()
    n_slices = st.getSize()
    st2 = ImageStack(st.getWidth(), st.getHeight(), n_slices)

    # Apply Gaussian blur and thresholding to every frame
    for sl in range(1, n_slices + 1):
        sys.stdout.write('.')
        ip = st.getProcessor(sl)
        blur.blurGaussian(ip, sigma, sigma, 0.02)
        ip2 = ip.convertToByteProcessor()
        ip2.threshold(threshold)
        ip2.invert()
        st2.setProcessor(ip2, sl)
    sys.stdout.write('\n')
    # Wrap ImageStack with ImagePlus for a return value
    imp2 = ImagePlus("gray avg thresholded", st2)
    return imp2


# Find coordinates (center of mass) of cells.
def find_coordinates(imp):
    rt = Analyzer.getResultsTable()
    pa = ParticleAnalyzer(ParticleAnalyzer.SHOW_NONE,
                          Measurements.SLICE | Measurements.CENTER_OF_MASS | Measurements.AREA, rt, 300, 10000, 0, 1)
    n_slices = imp.getStackSize()
    # Runs ParticleAnalyzer on every frame
    for i in range(1, n_slices + 1):
        imp.setSlice(i)
        pa.analyze(imp)
    rt.show('Results of particle analyzer')
    return []


def main():
    IJ.open("/path/to/movie.avi")
    imp = IJ.getImage()
    imp2 = threshold(imp)
    # Area, XM, YM, and Slice are displayed in Result window.
    find_coordinates(imp2)
    imp2.show()
    print('Done')


main()