Re: Analyze particles ...: Help and bug

Posted by Rasband, Wayne (NIH/NIMH) [E] on May 26, 2010; 4:14pm
URL: http://imagej.273.s1.nabble.com/Analyze-particles-Help-and-bug-tp3688137p3688140.html

On May 26, 2010, at 8:07 AM, Tamjid wrote:

> 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.

In the 1.44b9 daily build you can generate the particle outlines by using the "In situ Show" option to display the outlines as an overlay and then drawing the overlay. Here is a JavaScript example:

  imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/blobs.gif");
  IJ.setAutoThreshold(imp, "Default");
  IJ.run(imp, "Analyze Particles...", "size=350 show=Outlines in_situ");
  ip = imp.getProcessor().duplicate();
  ip = ip.convertToByte(false);
  ip.setColor(Color.black);
  ip.fill();
  ip.setColor(Color.white);
  overlay = imp.getOverlay();
  overlay.drawPixels(ip); // requires 1.44b9 or later
  imp.setOverlay(null);
  imp.show();
  new ImagePlus("Outlines", ip).show();

-wayne

>
> 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=1
>
>
> As 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]
>>