problems with the function: analyse particles

[Kathrin Kolotzek]

Dear helper,

I am a beginner in working with ImageJ. I would be happy if someone can help me with my problem.

I am using microscopy pictures of a polished structure and want to determine the porousness of the samples.
I  checked the user guide and as far I can transform the image to a greyscale and set the treshhold. As I know these are the points I have to do before using "analyse particles".  If I do this, as a result I get the area percentage of all particles compared to the whole area. But is it possible to get the area percentage of every single particle?

Thanks in regard.
Sincerely yours,

 

Kathrin Kolotzek

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[kirill8910]

Hello!

When you have black and white thresholded image and you use Analyse particles isnt it you get the list of particles and their area?  Also, just in case, "Area" should be checked in the Set measurements menue!

I think when you use "measure" then you get total area of particles...

sorry if I didnt understand.

Kirill

[Lai Ding]

Hello, Kathrin,

  Check the "add to manager" box in "Analyze Particle" window.  All the detected objects will be stored in the ROI manager. Then you can do the measurements you prefer for each object.

 Best
Lai

Lai Ding, PhD | Optical Imaging Manager
Harvard NeuroDiscovery Center
Harvard Medical School
[phone]
http://www.neurodiscovery.harvard.edu/ 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kathrin Kolotzek
Sent: Wednesday, August 29, 2012 8:04 AM
To: [hidden email]
Subject: problems with the function: analyse particles

Dear helper,

I am a beginner in working with ImageJ. I would be happy if someone can help me with my problem.

I am using microscopy pictures of a polished structure and want to determine the porousness of the samples.
I  checked the user guide and as far I can transform the image to a greyscale and set the treshhold. As I know these are the points I have to do before using "analyse particles".  If I do this, as a result I get the area percentage of all particles compared to the whole area. But is it possible to get the area percentage of every single particle?

Thanks in regard.
Sincerely yours,

 

Kathrin Kolotzek

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[Christian Goosmann]

Hi Kathrin,
before you execute 'Analyze Particles' you get a dialog with choices. If
you check 'display results' you should get a table of measurements with
one line per particle. What measurements you do get depends on what
boxes are checked in 'Analyze>Set Measurements... .' If you miss any
parameters you can export everything into a spreadsheet program and do
the calculations there.
Another useful feature in 'Analyze Particles' is the dropbox called
'show'. It will get you a drawing of all the particles in the image.
Just change the setting to 'outlines'.
This should get you going if you are using a fairly up to date version
of ImageJ.
Christian

Kathrin Kolotzek wrote:

> Dear helper,
>
> I am a beginner in working with ImageJ. I would be happy if someone can help me with my problem.
>
> I am using microscopy pictures of a polished structure and want to determine the porousness of the samples.
> I  checked the user guide and as far I can transform the image to a greyscale and set the treshhold. As I know these are the points I have to do before using "analyse particles".  If I do this, as a result I get the area percentage of all particles compared to the whole area. But is it possible to get the area percentage of every single particle?
>
> Thanks in regard.
> Sincerely yours,
>
>  
>
> Kathrin Kolotzek
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Kathrin Kolotzek]

Hey Christian, Hey Larry

thanks for your quick respons.

We are having an alloy which is pressed out of grains. And depending the parameters there are sometimes more and bigger pores and sometimes not. So  I want to determine the  porosity depending the used parameters.
Furthermore I am interested in the percentage area of the particles  to sort them better out.

Christian I think u mean something like this here: (I shortend it and just listets area and %area) right?

   Area       %area
1    12        100
2    12        100
3    12        100
4    446       100
5    12        100


And here I was wondering why it always says 100% in %area, no matter what size the particle has.
So do I have this right, in your opinion I should just take the values which are presented in the gap "area" and calculate the %area on my own?

Thanks in regard.
Kathrin

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[Christian Goosmann]

Hi Kathrin,
hey, you got me surprised. The area fraction shows 100% for each
particle also when I try it with the blob sample from the ImageJ file
menu. It seems also to be dependent on the scaling set in 'Analyze>set
scale...' . Maybe one of the programmers know why the area fraction is
not expressed as fraction of the whole image which would be what I'd
expect. For the time being a workaround for you is to get the total area
of your frame from the image information or by selecting the whole image
(ctl+a) and making a measurement (ctl+m). With this figure you can
calculate each fraction of a particle in an excel  or calc -table.
By the way, have you noticed that the results menu in the results window
can show you a histogram of the distribution in your measurements? Maybe
that is also useful for you.
Good luck
Christian

Kathrin Kolotzek wrote:

> Hey Christian, Hey Larry
>
> thanks for your quick respons.
>
> We are having an alloy which is pressed out of grains. And depending the parameters there are sometimes more and bigger pores and sometimes not. So  I want to determine the  porosity depending the used parameters.
> Furthermore I am interested in the percentage area of the particles  to sort them better out.
>
> Christian I think u mean something like this here: (I shortend it and just listets area and %area) right?
>
>     Area       %area
> 1    12        100
> 2    12        100
> 3    12        100
> 4    446       100
> 5    12        100
>
>
> And here I was wondering why it always says 100% in %area, no matter what size the particle has.
> So do I have this right, in your opinion I should just take the values which are presented in the gap "area" and calculate the %area on my own?
>
> Thanks in regard.
> Kathrin
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Jan Eglinger]

Hi Christian and Kathrin,

the Area fraction is determined as the percentage of area above
threshold within the current ROI (or the entire image if no selection is
active). I guess that's the reason why 'analyse particles' shows 100%
area fraction for each particle, because each particle is a single ROI,
and 100% of that particle are above threshold.

Jan



On 30.08.2012 10:27 AM, Christian Goosmann wrote:

> Hi Kathrin,
> hey, you got me surprised. The area fraction shows 100% for each
> particle also when I try it with the blob sample from the ImageJ file
> menu. It seems also to be dependent on the scaling set in 'Analyze>set
> scale...' . Maybe one of the programmers know why the area fraction is
> not expressed as fraction of the whole image which would be what I'd
> expect. For the time being a workaround for you is to get the total area
> of your frame from the image information or by selecting the whole image
> (ctl+a) and making a measurement (ctl+m). With this figure you can
> calculate each fraction of a particle in an excel  or calc -table.
> By the way, have you noticed that the results menu in the results window
> can show you a histogram of the distribution in your measurements? Maybe
> that is also useful for you.
> Good luck
> Christian
>
> Kathrin Kolotzek wrote:
>> Hey Christian, Hey Larry
>>
>> thanks for your quick respons.
>>
>> We are having an alloy which is pressed out of grains. And depending
>> the parameters there are sometimes more and bigger pores and sometimes
>> not. So  I want to determine the  porosity depending the used parameters.
>> Furthermore I am interested in the percentage area of the particles
>> to sort them better out.
>>
>> Christian I think u mean something like this here: (I shortend it and
>> just listets area and %area) right?
>>
>>     Area       %area
>> 1    12        100
>> 2    12        100
>> 3    12        100
>> 4    446       100
>> 5    12        100
>>
>>
>> And here I was wondering why it always says 100% in %area, no matter
>> what size the particle has.
>> So do I have this right, in your opinion I should just take the values
>> which are presented in the gap "area" and calculate the %area on my own?
>>
>> Thanks in regard.
>> Kathrin
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Barbara]

Hi,

I am having the same problem as Kathrin and came across this conversation. Is the conclusion that there is no simple way to have %area calculated by ImageJ then? In other words, one has to calculate it self?
Thanks,

Barbara

[AaronUCF2014]

If you change to an 8-bit image or RGB stack, this will change.
You can play around with inverting the image and then converting to an RGB stack and then setting a threshold. Then making an ROI and measuring to get %Area, which gives the percent of that area meeting the defined threshold.
If all images are acquired in the exact same manner and then processed in this manner with the same threshold set, it should give relatively quantitative measurements.