ImageJ Jython: draft cell segmentation protocol

cell_segmentation.py

#!/usr/bin/env jython

#  \begin{enumerate}
#    \item Process $\rightarrow$ Gaussian Blur
#    \item Process $\rightarrow$ Enhance Contrast (normalize \& equalize histogram)
#    \item Image $\rightarrow$ Type $\rightarrow$ HSB stack
#    \item Image $\rightarrow$ Stacks $\rightarrow$ Stack to images
#    \item keep only the Hue image
#    \item Process $\rightarrow$ Find maxima... (noise tolerance 60)
# \end{enumerate}

from ij import IJ, measure
from ij.plugin.filter import ParticleAnalyzer
from ij.plugin.frame import RoiManager
from ij.process import ImageProcessor
from java.lang import Double
import sys

# http://pacific.mpi-cbg.de/wiki/index.php/Jython_Scripting#Jython_tutorials_for_ImageJ

def cell_counter(stack_file):
    img_stack = IJ.openImage( stack_file )
    IJ.run( img_stack, "Smooth", "stack" )
    IJ.run( img_stack, "Sharpen", "stack" )
    IJ.setAutoThreshold(img_stack, "Default")
    IJ.run( img_stack, "Convert to Mask", "calculate black")
    img_stack.getProcessor().invert()
    
    img_stack.show()
    
    # Create a table to store the results
    #table = measure.ResultsTable()
    
    # Create a hidden ROI manager, to store a ROI for each blob or cell
    #roim = RoiManager(True)
    # Create a ParticleAnalyzer, with arguments:
    # 1. options (could be SHOW_ROI_MASKS, SHOW_OUTLINES, SHOW_MASKS, SHOW_NONE, ADD_TO_MANAGER, and others; combined with bitwise-or)
    # 2. measurement options (see [http://rsb.info.nih.gov/ij/developer/api/ij/measure/Measurements.html Measurements])
    # 3. a ResultsTable to store the measurements
    # 4. The minimum size of a particle to consider for measurement
    # 5. The maximum size (idem)
    # 6. The minimum circularity of a particle
    # 7. The maximum circularity

    stack = img_stack.getStack()

    for i in range( 1,img_stack.getStackSize()+1):
        stack.getProcessor(i).invert()
        table = measure.ResultsTable()
        pa = ParticleAnalyzer( ParticleAnalyzer.SHOW_OVERLAY_OUTLINES  | ParticleAnalyzer.INCLUDE_HOLES,
                               measure.Measurements.AREA | measure.Measurements.AREA_FRACTION | measure.Measurements.MEAN,
                               table,
                               200,
                               Double.POSITIVE_INFINITY,
                               0.0,
                               1.0 )
        #pa.setHideOutputImage(True)
        pa.analyze(img_stack, stack.getProcessor(i))
        #print table.getRowAsString(-1)
        # k=0
        # while (table.getColumnHeading(k)!= None):
        #     if table.columnExists(k):
        #         print k, table.getColumnHeading(k), table.getColumn(k)
        #     k += 1
        if table.columnExists(0):
            print i, len(table.getColumn(0))
 
    # if pa.analyze(img_stack):
    #     print "All ok"
    # else:
    #     print "There was a problem analyzing", img_stack
  
    # IJ.run( img_stack, "Analyze Particles...", "size=200-Infinity circularity=0.00-1.00 show=Outlines include summarize record stack")
    # IJ.run("Measurements...",  "toto" + ".pts")
    #return table

table = cell_counter(sys.argv[1])

# print table.getColumnHeadings() 
# for row in table.getColumn(0):
#    print row