Find cells in all frames from a movie, which can run in headless mode of Fiji

find_cells-headless.fiji.py

# This script runs on Fiji.
# Just drag and drop this file into a Fiji window.
# You can also use headless mode
# > /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless \
# > find_cells-headless.fiji.py /path/to/movie.avi

from ij import IJ, ImageStack, ImagePlus
from ij.process import ImageProcessor, ImageConverter
from ij.plugin import ImageCalculator, AVI_Reader, ZProjector, HyperStackConverter
from ij.plugin.filter import GaussianBlur, Analyzer, ParticleAnalyzer
from ij.measure import Measurements, ResultsTable
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.flush()
    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.
# Return (header as [str], data as [[str]])
# Each row of data has [Number, Area, XM, YM, Slice]
def find_coordinates(imp):
    # rt = Analyzer.getResultsTable()
    rt = ResultsTable()
    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)
    ps = []
    heading = ['Number'] + list(rt.getHeadings())
    # Get all results from ResultsTable
    for i in range(rt.getCounter()):
        ps.append(rt.getRowAsString(i).split('\t'))
    return heading, ps


def main():
    # 1st command line argument is a path of input movie.
    in_path = sys.argv[1] if len(
        sys.argv) >= 2 else "/path/to/default_movie.avi"
    out_path = in_path.replace('raw data', 'visualizer').replace('.avi', '.csv')

    print('Input: ' + in_path)
    print('Output: ' + out_path)

    print('Script loaded.')
    imp = AVI_Reader().openVirtual(in_path)
    print('Movie loaded. Thresholding...')
    imp2 = threshold(imp)
    print('Thresholded. Finding coordinates...')
    heading, ps = find_coordinates(imp2)
    print('Found coordinates.')

    # Write out coordinates as a csv file.
    import csv
    f = open(out_path, 'wb')
    writer = csv.writer(f)
    writer.writerow(heading)
    for row in ps:
        writer.writerow(row)
    f.close()
    print('CSV written to: ' + out_path)
    print('Done')


main()