Posted by
Md Tamjidul Hoque on
May 26, 2010; 12:07pm
URL: http://imagej.273.s1.nabble.com/Analyze-particles-Help-and-bug-tp3688137p3688139.html
Thanks Wayne and Stoyan.
However, Wayne, I see the output differs compared to
(a) Outlines in 'Analyze particles' vs. (b) Masks in 'Analyze
particles' and then Process>Binary>Outline.
For example, for an images (Image #0:
http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/0_Intermediateimage.zip?attredirects=0&d=1)
with object based on size first, I am making a superset of the objects
outlined in red and numbers (Image #1:
http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/1_CountAllbySize.zip?attredirects=0&d=1).
Then I am defining circularity (say .8 to 1.0) and is running the (a)
Outlines in 'Analyze particles' in green remaining other parameter unchanged
and then adding with the Image #1, so that I can get red outlined object
outside the circularity range and yellow (red+green) inside the circularity
range.
And as the objects are already numbered before (in Image #1) I was trying to
get the outlined image without the object being numbered in the circularity
based 2nd case.
See the outcome, image # 2:
http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/2_CircularitybasedsubsetOutlinefirst.zip?attredirects=0&d=1As an alternate approach, as you have suggested to Masks in 'Analyze
particles' and then Process>Binary>Outline:
I had applied the Masks in 'Analyze particles' on Image# 0 and then
Process>Binary>Outline and greened ...
But, the outputs differ and the outlined of the circularity set is not fully
overlapped with the previous outline as generated in image #1.
So the outcome looks distorted (image #4:
http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/3_CircularitybasedsubsetMaskfirst.zip?attredirects=0&d=1)
and for some images/case the outputs look very bad.
So, please help on this issue. I am not sure if it is due to different
line-thickness or different outlining algorithms ....
or, it would also have been better to have an option with the 'Analyze
particles' to tick for number-less outlined object.
Thanks
Tamjid
> (1)You could use the Show: "Masks" option and then run
Process>Binary>Outline.
> -wayne
On Wed, May 26, 2010 at 6:03 PM, Stoyan Pavlov <
[hidden email]>wrote:
> Hi Tamjidul,
>
> > (2) Possible bug: The number kept on increasing within the outlined
> image
> > when you repeatedly 'Analyze particles...'.
>
> It is not a bug! If you want a new numbering to start, you have to
> select "clear results" from the "Analyze particles ..." window.
>
> Stoyan Pavlov
>
>
> 2010/5/26 Md Tamjidul Hoque <
[hidden email]>:
> > Hi All
> >
> > (1) I need help: How can I turn off the numbering of the outlined
> objects
> > while using 'Analyze particles...'?
> >
> > (2) Possible bug: The number kept on increasing within the outlined
> image
> > when you repeatedly 'Analyze particles...'.
> > I was surprised to see that even if I close
> the
> > particular image and then reopen (apply Otsu Thresholding 8 bit) and
> reapply
> > 'Analyze particles...', the number starts from/after the last maximum
> > number.
> > I had to restart ImageJ to get rid of the
> > problem.
> >
> > Probably it will have to reinitialize its
> count
> > variable every time 'Analyze particles...' is applied.
> >
> >
> > Thanks
> > Tamjid
> >
>
>
>
> --
> Dr. Stoyan P. Pavlov, MD
> 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 - 050 #2638
> e-mail:
[hidden email]
>