Re: Shadows, leaf morphology problem

Posted by Stoyan Pavlov on Dec 13, 2013; 8:05am
URL: http://imagej.273.s1.nabble.com/Shadows-leaf-morphology-problem-tp5005891p5005902.html

Since you know the maximum size of the particles you wish to analyse, you
can also try some form of morphological filtering. Give a try to the
"Granulometric filtering plugin" by Dimiter Prodanov (
http://rsbweb.nih.gov/ij/plugins/gran-filter.html). If it doesn't work for
you , you can try Top-Hat opening by reconstruction:

1. Run a small size median filter (2.0) to get rid of the noise
2. Run a Minimum filter on your image with size corresponding to the
biggest particles you want to keep.(this way you get rid of the bigger
particles, but it also degrades the image).
3. Reconstruct the Filtered image (using Greyscale reconstruct from
Landini's Morphological plugins set (
http://www.dentistry.bham.ac.uk/landinig/software/software.html) with mask
the original image and seed the Minimum filtered image. Now you have a
representation of your background. (original picture but just without the
particles)
4. Run if necessary a median filter (2.0) on the reconstructed background
to get rid of noise.
5. Subtract the Reconstructed background image from your original (median
filtered) image.
Now this leaves only the particles of the size you need and a small part of
the ridges. You can get rid off the latter adjusting the conditions of the
Particle analyzer - Size and/or circularity.
If this approach works for you, there is a ready to use macro in Gabriel
Landini's "Morphological Operators for ImageJ" set (Top-Hat opening by
reconstruction) .




---
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 052
e-mail: [hidden email]
           [hidden email]

Zentrum für Anatomie
Uniklinik Köln
[hidden email]
Tel: [phone]





2013/12/12 Adam Hughes <[hidden email]>

> A good first approach would be to try an auto-local threshold, which will
> be able to handle the contrast disparity.
>
> http://fiji.sc/Auto_Local_Threshold
>
> If you have imageJ 1.48, this might already be in your threshold settings.
>
> Try out the 3x3 plot as shown in the link and see if any of the methods
> give you the image you want.  If not, then it becomes more tricky.
>
>
> On Thu, Dec 12, 2013 at 4:06 PM, Leaf Pollution <
> [hidden email]
> > wrote:
>
> > <http://imagej.1557.x6.nabble.com/file/n5005893/s.acre_200_%282%29.jpg>
> > <
> http://imagej.1557.x6.nabble.com/file/n5005893/thresholded_s.acre_200.jpg
> > >
> >
> > Another problem occuring is with the brightness created from the ESEM-
> seen
> > on the third image, the thresholding is ineffective and particles cannot
> be
> > distinguished (image 4)
> >
> > Thanks for your help.
> >
> >
> >
> > <http://imagej.1557.x6.nabble.com/file/n5005893/S.acre_100.jpg>
> > <
> http://imagej.1557.x6.nabble.com/file/n5005893/S.acre_100_thresholded.jpg
> > >
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/Shadows-leaf-morphology-problem-tp5005891p5005893.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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