Analyze particles ...: Help and bug

[Md Tamjidul Hoque]

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

[Stoyan Pavlov]

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]

[Md Tamjidul Hoque]

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=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]
>

[Gabriel Landini]

On Wednesday 26 May 2010  14:16:58 you wrote:
> 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_Ci
> rcularitybasedsubsetMaskfirst.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 ....

I think that this may be due to a known mismatch of the outlines of a ROI with
the pixels of a ROI. This was raised recently in the fiji-devel list.
I do not think that there is a solution currently unless you treat the blobs
in the same way.

My suggestion is to make your own routine to draw the boundaries of ROIs as
the pixels that  touch the background. For example, assuming white objects on
a black background:

setBatchMode(true);
a=getTitle();
run("Duplicate...", "title=test-1");
selectWindow("test-1");
run("Minimum...", "radius=0.5");
imageCalculator("Subtract", a,"test-1");
setBatchMode(false);

You can do this also with Binary Thinning in a 1 line macro:

run("BinaryThin ", "kernel_a='2 1 2 1 1 1 2 1 2 ' rotations='none'
iterations=1 white");

This guarantees that all the pixels of the boundary of the blob are contained
in the blob that you see.
Otherwise, IJ  gets the ROI of the blob and draws the outline which in not
completely contained in the blob.

If you want to show certain blobs, then use the XStart YStart coordinates to
produce an image with only those pixels set and use the BinaryRreconstruct
plugin in my page to recreate only those particles (the seed is the points you
set and the mask is the original binary image).

Cheers
G

[Rasband, Wayne (NIH/NIMH) [E]]

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]
>>

[Md Tamjidul Hoque]

Rasband, Wayne (NIH/NIMH) [E] wrote:

> 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
>
>  

Dear Wayne

      I think the other theme behind the 'in_situ" was not to open the
window (specially for the batch mode) and to apply the output to current
imp .    

Now with the current change in 1.44b9, I could not figure out how can I
get a outlined and numbered object using "in_situ" for 'Analyze
Particles ...' (such as Image#1) ?

Because, "in_situ" mode I have to generate (a) outlined and numbered
objects as well as (b) outlined and non-numbered objects,

so that I can have

Image #1:(http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/1_CountAllbySize.zip?attredirects=0&d=1)

as previously it was possible to get Image#1 which is not working now with the updated version 1.44b9 in "in_situ" mode).

But I can have Image #4:(http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/4_Circularitybasedsubsetoutlinedinsitu.zip?attredirects=0&d=1)
now.


So, I can add Image #1 and Image #4 to form the final result (Image # 5:
http://sites.google.com/site/tamjidulhoque/home/resume-of/useful-links/5_finalResultof1add4.zip?attredirects=0&d=1).

But again he problem is I can not get Image #1 in 'in_situ' mode.

Thanks
Tamjid

>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>    

[Md Tamjidul Hoque]

Thanks Gabriel to clarify the problem and for providing the suggestion.

-Tamjid

Gabriel Landini wrote:

> On Wednesday 26 May 2010  14:16:58 you wrote:
>  
>> 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_Ci
>> rcularitybasedsubsetMaskfirst.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 ....
>>    
>
> I think that this may be due to a known mismatch of the outlines of a ROI with
> the pixels of a ROI. This was raised recently in the fiji-devel list.
> I do not think that there is a solution currently unless you treat the blobs
> in the same way.
>
> My suggestion is to make your own routine to draw the boundaries of ROIs as
> the pixels that  touch the background. For example, assuming white objects on
> a black background:
>
> setBatchMode(true);
> a=getTitle();
> run("Duplicate...", "title=test-1");
> selectWindow("test-1");
> run("Minimum...", "radius=0.5");
> imageCalculator("Subtract", a,"test-1");
> setBatchMode(false);
>
> You can do this also with Binary Thinning in a 1 line macro:
>
> run("BinaryThin ", "kernel_a='2 1 2 1 1 1 2 1 2 ' rotations='none'
> iterations=1 white");
>
> This guarantees that all the pixels of the boundary of the blob are contained
> in the blob that you see.
> Otherwise, IJ  gets the ROI of the blob and draws the outline which in not
> completely contained in the blob.
>
> If you want to show certain blobs, then use the XStart YStart coordinates to
> produce an image with only those pixels set and use the BinaryRreconstruct
> plugin in my page to recreate only those particles (the seed is the points you
> set and the mask is the original binary image).
>
> Cheers
> G
>
>  

[Rasband, Wayne (NIH/NIMH) [E]]

Here is JavaScript that demonstrates how to use the new particle analyzer show="Overlay Outlines" and "In situ Show" options, and the Overlay.setStrokeColor() method, which are available in the 1.44b11 daily build. Note that the particle analyzer now respects the "Black background" flag when the "In situ Show" option is used.
 
  imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/blobs.gif");
  IJ.setAutoThreshold(imp, "Default");
  Prefs.blackBackground = true;
  IJ.run(imp, "Analyze Particles...",
     "size=500 show=[Overlay Outlines] clear exclude");
  overlay = imp.getOverlay();
  IJ.run(imp, "Analyze Particles...",
     "size=0 show=Outlines clear in_situ exclude");
  overlay.setStrokeColor(Color.yellow);
  overlay.drawLabels(false);
  imp = imp.flatten();
  imp.show();

[Md Tamjidul Hoque]

Dear Wayne

              the code is simpler and great ...

By the way, is there a way to check, how many particles are detected?

For example,

... size=5000 instead of ... size=500 it will cause trouble/ will crash,
so, like to check how many particles are detected to avoid rest of the process while particle count =0.

Thanks
Tamjid



Rasband, Wayne (NIH/NIMH) [E] wrote:

> Here is JavaScript that demonstrates how to use the new particle analyzer show="Overlay Outlines" and "In situ Show" options, and the Overlay.setStrokeColor() method, which are available in the 1.44b11 daily build. Note that the particle analyzer now respects the "Black background" flag when the "In situ Show" option is used.
>  
>   imp = IJ.openImage("http://rsb.info.nih.gov/ij/images/blobs.gif");
>   IJ.setAutoThreshold(imp, "Default");
>   Prefs.blackBackground = true;
>   IJ.run(imp, "Analyze Particles...",
>      "size=500 show=[Overlay Outlines] clear exclude");
>   overlay = imp.getOverlay();
>   IJ.run(imp, "Analyze Particles...",
>      "size=0 show=Outlines clear in_situ exclude");
>   overlay.setStrokeColor(Color.yellow);
>   overlay.drawLabels(false);
>   imp = imp.flatten();
>   imp.show();
>
>  

[Arne Seitz]

 Dear List,

currently I'm facing the problem that avi-files generated with ImageJ (Version 1.44a; Java 1.6.0_10) cannot be opened with Windows Media Player from Windows 7. I don't care about Windows Mediaplayer but it is also not possible to use these avi files in presentations which is a little bit nasty. Has maybe anyone encountered the same problem and/or a solution for this issue.

Thanks for your help

Cheers Arne


---------------------------------------------------------------
Dr. Arne Seitz
Head of Bioimaging and Optics Platform (BIOP)
Swiss Institute of Technology (EPFL)
Faculty of Life Sciences
Station 15, AI 0241
CH-1015 Lausanne

Phone: [phone]
Fax:      [phone]
http://biop.epfl.ch/
---------------------------------------------------------------


 

[Michael Schmid]

On 28 May 2010, at 10:04, Seitz Arne wrote:

>  Dear List,
>
> currently I'm facing the problem that avi-files generated with  
> ImageJ (Version 1.44a; Java 1.6.0_10) cannot be opened with Windows  
> Media Player from Windows 7. I don't care about Windows Mediaplayer  
> but it is also not possible to use these avi files in presentations  
> which is a little bit nasty. Has maybe anyone encountered the same  
> problem and/or a solution for this issue.
>
> Thanks for your help
>
> Cheers Arne

Hi Arne,

which type of compression do you use? PNG has the advantage of being  
non-lossy and smaller than uncompressed, but there are many programs  
that cannot read it.
Also, some programs cannot read avi files if the image width and  
height are not multiples of 4.

Michael

[Arne Seitz]

On 28 May 2010, at 10:04, Seitz Arne wrote:

>  Dear List,
>
> currently I'm facing the problem that avi-files generated with  
> ImageJ (Version 1.44a; Java 1.6.0_10) cannot be opened with Windows  
> Media Player from Windows 7. I don't care about Windows Mediaplayer  
> but it is also not possible to use these avi files in presentations  
> which is a little bit nasty. Has maybe anyone encountered the same  
> problem and/or a solution for this issue.
>
> Thanks for your help
>
> Cheers Arne

Hi Arne,

which type of compression do you use? PNG has the advantage of being  
non-lossy and smaller than uncompressed, but there are many programs  
that cannot read it.
Also, some programs cannot read avi files if the image width and  
height are not multiples of 4.

Michael

Hi Michael,

Thanks for your hints. The problem was caused due to the wrong image format.

Cheers Arne

[Rasband, Wayne (NIH/NIMH) [E]]

>Dear List,
>
> Currently I'm facing the problem that avi-files generated with ImageJ
> (Version 1.44a; Java 1.6.0_10) cannot be opened with Windows
> Media Player from Windows 7. I don't care about Windows Mediaplayer
> but it is also not possible to use these avi files in presentations which
> is a little bit nasty. Has maybe anyone encountered the same
> problem and/or a solution for this issue.

The ImageJ 1.44b12 daily build fixes a bug that caused 8 and 16 bit grayscale stacks saved as JPEG-compressed AVIs to not play correctly in the Windows 7 Media Player.

-wayne