http://imagej.273.s1.nabble.com/grayscale-distrib-whole-stack-tomograph-tp3685571p3685573.html
1. do you know how to export the histogram-stack in tabular form xyz?
2. how to modify the code to get histogram on a round selection of the
>
>
> Begin forwarded message:
>
> >
> > Date: Tue, 22 Feb 2011 15:22:59 +0100
> > From: Alessandro Zivelonghi <
[hidden email]>
> > Subject: grayscale distrib. whole stack (tomograph)
> >
> > Hello There,
> >
> > I have a question as a beginner with imageJ/fiji.
> >
> > Somebody knows how to :
> > - extract with imageJ/fiji the grayscale distribution of ALL the slices
> of a
> > stack (tomograph) and build up a xyz function, with xy assigned to the
> > grayscale distr. and z being the heigth of the specimen?
> >
> >
> > I know how to get the xy distrib. of a slice (adjust/threshold) but I
> don't
> > know how to export it in tabular form.
> > my 3D stack is 8 bit grayscale.
>
> try putting this jython script into the fiji script editor and running it.
> (select language python / jython
>
> # Time_Series_Histogram.py
> # this script makes the histogram for each frame of a movie
> # and as it goes adds (concatenates) each one into a single movie stack
>
> # Dan White and Silke Gerwig MPI-CBG
> # Aug 2009-2011
>
> #!/usr/bin/env python
>
> from ij import IJ, ImagePlus
> # the current image
> imp = IJ.getImage()
> stack = imp.getStack()
>
> # for all the frames in the movie, run histogram
> for i in range(1, imp.getNSlices() + 1): # remember a python range (1, 10)
> is the numbers 1 to 9!
> #getNSlices not getNFrames since input data is a 3D stack not a time series
> stack.
> slice = ImagePlus(str(i), stack.getProcessor(i))
> # Execute plugin exactly on this slice i
> IJ.run(slice, "Histogram", "slice")
> # concatenate the new histogram onto the end of the histogram stack we
> want in the end, but not if its then 1st one!
>
> if i == 1:
> pass
> else:
> IJ.run("Concatenate...", "stack1=[Histogram of 1] stack2=[Histogram of "
> + str(i) + "] title=[Histogram of 1]")
>
> IJ.log("Done!")
> >
> > Many thanks,
> > bye!
> > Alex
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
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> Included)
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> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
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