Isolating the background pixels from foreground pixels

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Isolating the background pixels from foreground pixels

Geology Guy
Good Afternoon Everyone,
I  am trying to calculate Area of objects (foreground pixels) in image J but it is not working as I hoped it would have. After thresholding and converting to a binary image, I tried to calculate the Area of the objects but the background pixels are being included in the Area Calculation. Is there a way to solve this problem? Thanks for your response
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Re: Isolating the background pixels from foreground pixels

karo03
Have a look into Edit->Options->Colors…
Maybe there is the explanation for this behavior.

Regards
Karsten
 
Am 04.07.2013 um 22:15 schrieb Geology Guy <[hidden email]>:

> Good Afternoon Everyone,
> I  am trying to calculate Area of objects (foreground pixels) in image J but
> it is not working as I hoped it would have. After thresholding and
> converting to a binary image, I tried to calculate the Area of the objects
> but the background pixels are being included in the Area Calculation. Is
> there a way to solve this problem? Thanks for your response
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Re: Isolating the background pixels from foreground pixels

Geology Guy
In reply to this post by Geology Guy
Dear Karsten,
Thanks for your response. I checked the Edit> Options> Colors and the background is black while the Foreground is White. This is what I expect because after reading the Image J manual, I learnt that Image J only makes calculations from binary images when the background is black and the foreground is white.

I am using the default thresholding (i.e. AUTO) and checked the DARK BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE BACKGROUND". Again this setting that I am using is because the Image J manual recommended a background that is black and white foreground in order to be able to carry out calculations involving binary imaging. Or am I wrong somewhere maybe that's why the background pixels are getting picked up in the foreground when I try to calculate Area for foreground objects ONLY? Thanks for your help.

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Re: Isolating the background pixels from foreground pixels

karo03
Hi Geology Guy, possibly geologists think different.

There are gray or color images with bright background and others with a dark background. This should not be mixed up with the representation of binary images. Foreground is always the set of pixels which are thresholded (shown with the small box) in the histogram of the interactive thresholding window. They get a value of 255. The background gets 0. Still by the Options->Colors… you can select the representation of foreground and background pixels.

Maybe some clarification for you?

Karsten

(I have to confess that I rarely read manuals, I prefer trial and error)

Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
> Thanks for your response. I checked the Edit> Options> Colors and the
> background is black while the Foreground is White. This is what I expect
> because after reading the Image J manual, I learnt that Image J only makes
> calculations from binary images when the background is black and the
> foreground is white.
>
> I am using the default thresholding (i.e. AUTO) and checked the DARK
> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box
> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
> BACKGROUND". Again this setting that I am using is because the Image J
> manual recommended a background that is black and white foreground in order
> to be able to carry out calculations involving binary imaging. Or am I wrong
> somewhere maybe that's why the background pixels are getting picked up in
> the foreground when I try to calculate Area for foreground objects ONLY?
> Thanks for your help.
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Karsten
[hidden email]

--
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Re: Isolating the background pixels from foreground pixels

Geology Guy
Hello again Karsten,
Thanks for your reply. I am not quite sure that I understand the things you asked me to do so I will look at your reply again and read the section of the manual on thresholding and binary images and see if I can figure it out.

Thanks a lot for your help
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Re: Isolating the background pixels from foreground pixels

Rasband, Wayne (NIH/NIMH) [E]
In reply to this post by Geology Guy
On Jul 4, 2013, at 4:49 PM, Geology Guy wrote:

> Dear Karsten,
> Thanks for your response. I checked the Edit> Options> Colors and the
> background is black while the Foreground is White. This is what I expect
> because after reading the Image J manual, I learnt that Image J only makes
> calculations from binary images when the background is black and the
> foreground is white.

This is not correct. To eliminate ambiguity, it is best to use Image>Adjust>Threshold to threshold images to be measured using the Measure command and the particle analyzer. Measurements done by Analyze>Measure are limited to thresholded pixels when "Limit to Threshold" is enabled in Analyze>Set Measurements.

-wayne

> I am using the default thresholding (i.e. AUTO) and checked the DARK
> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box
> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
> BACKGROUND". Again this setting that I am using is because the Image J
> manual recommended a background that is black and white foreground in order
> to be able to carry out calculations involving binary imaging. Or am I wrong
> somewhere maybe that's why the background pixels are getting picked up in
> the foreground when I try to calculate Area for foreground objects ONLY?
> Thanks for your help.
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
> Sent from the ImageJ mailing list archive at Nabble.com.

--
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Re: Isolating the background pixels from foreground pixels

Geology Guy
In reply to this post by karo03

Dear Karsten,

I am trying to measure the parameters of 100 particles in Image J and under "Analyze Particles", I also selected the "Summary option". My main problem now is that I deleted some of the particles as requested by my Professor from the list after the data was provided by Image J. This makes the "Summary" data not useful anymore as they do not reflect all the 100 particles I started with originally. I measured all the parameters under "Set measurement" for each particle so now I need to produce a new summary data as the values would be used in plotting graphs. I have figured out how to Area which is just a simple addition of the areas of each particle. Other parameters that are in the summary that I cannot determine from the particles data are the following:

 

 

 

Perim.

Major

Minor

Circ.

Solidity

Feret

FeretX

FeretY

FeretAngle

MinFeret

IntDen

Median

Skew

Kurt

 

I have attached 2 Excel spreadsheets. The first shows my original particles data and the highlighted rows in yellow are rows that I have deleted their data as they are bad data. I am working on my research that is due on the 31st of this month so this is very urgent. Thank you very much for your assistance. 


Yours faithfully,

Tola



On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <[hidden email]> wrote:
Hi Geology Guy, possibly geologists think different.

There are gray or color images with bright background and others with a dark background. This should not be mixed up with the representation of binary images. Foreground is always the set of pixels which are thresholded (shown with the small box) in the histogram of the interactive thresholding window. They get a value of 255. The background gets 0. Still by the Options->Colors… you can select the representation of foreground and background pixels.

Maybe some clarification for you?

Karsten

(I have to confess that I rarely read manuals, I prefer trial and error)

Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
> Thanks for your response. I checked the Edit> Options> Colors and the
> background is black while the Foreground is White. This is what I expect
> because after reading the Image J manual, I learnt that Image J only makes
> calculations from binary images when the background is black and the
> foreground is white.
>
> I am using the default thresholding (i.e. AUTO) and checked the DARK
> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box
> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
> BACKGROUND". Again this setting that I am using is because the Image J
> manual recommended a background that is black and white foreground in order
> to be able to carry out calculations involving binary imaging. Or am I wrong
> somewhere maybe that's why the background pixels are getting picked up in
> the foreground when I try to calculate Area for foreground objects ONLY?
> Thanks for your help.
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Karsten
[hidden email]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html



If you reply to this email, your message will be added to the discussion below:
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W06.08_20 ParticleData.xls (50K) Download Attachment
W06.08_20 Summary of Particle Data.xls (446 bytes) Download Attachment
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Re: Isolating the background pixels from foreground pixels

Gabriel Landini
On Saturday 27 Jul 2013 02:47:33 you wrote:

> Dear Karsten,
>
> I am trying to measure the parameters of 100 particles in Image J and under
> "Analyze Particles", I also selected the "Summary option". My main problem
> now is that I deleted some of the particles as requested by my Professor
> from the list after the data was provided by Image J. This makes the
> "Summary" data not useful anymore as they do not reflect all the 100
> particles I started with originally. I measured all the parameters under
> "Set measurement" for each particle so now I need to produce a new summary
> data as the values would be used in plotting graphs. I have figured out how
> to Area which is just a simple addition of the areas of each particle.
> Other parameters that are in the summary that I cannot determine from the
> particles data are the following:

I would question the use of a summary, if you do not know what it means.
The best thing is to generate your own summary using the spreadsheet functions
(excel? SPSS? R?) to output distribution descriptor (means, sd, min, max,
etc.) that then I can use for a particular purpose.

For example, Feret angle cannot be just "averaged" to estimate an average
angle.
Feret X and Y are perhaps coordinates. What use is that?

--
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Re: Isolating the background pixels from foreground pixels

karo03
In reply to this post by Geology Guy
Hi Geology Guy,

Seemingly you have switched on all features. For the shape of particles there are IMHO only senseful:

Area (*)
Perimeter (*)
Circ (*)
Solidity (*)
Round (*)
Feret (*)
MinFeret
Minor/Major

all others are related to redirection to gray scale image or not really helpful for particle shape description, better for representation e.g. by ellipsoids.

To summarize a set of particles:

The features (*) can be summarized by the usual Mean and SD.
 
Min Feret is special, either the (global) Minimum or the span (Max-Min) could characterize the set os particles.

Feret Angle and Angle might be helpful for elongated particles, but the mean of angles is a difficult task since angles come from a number module. (to difficult for the available time!)

The mean of (Minor/Major), a ratio estimator is mean(Minor)/mean(Major) not mean(Minor/Major). SD of the ratio is a bit complicated too!

I think this list of features should be enough for characterization of a set of particles!

Hope that helps a bit

Regards
Karsten

Am 27.07.2013 um 03:47 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
>
> I am trying to measure the parameters of 100 particles in Image J and under
> "Analyze Particles", I also selected the "Summary option". My main problem
> now is that I deleted some of the particles as requested by my Professor
> from the list after the data was provided by Image J. This makes the
> "Summary" data not useful anymore as they do not reflect all the 100
> particles I started with originally. I measured all the parameters under
> "Set measurement" for each particle so now I need to produce a new summary
> data as the values would be used in plotting graphs. I have figured out how
> to Area which is just a simple addition of the areas of each particle.
> Other parameters that are in the summary that I cannot determine from the
> particles data are the following:
>
>
>
>
>
>
>
> Perim.
>
> Major
>
> Minor
>
> Circ.
>
> Solidity
>
> Feret
>
> FeretX
>
> FeretY
>
> FeretAngle
>
> MinFeret
>
> IntDen
>
> Median
>
> Skew
>
> Kurt
>
>
>
> I have attached 2 Excel spreadsheets. The first shows my original particles
> data and the highlighted rows in yellow are rows that I have deleted their
> data as they are bad data. I am working on my research that is due on the
> 31st of this month so this is very urgent. Thank you very much for your
> assistance.
>
>
> Yours faithfully,
>
> Tola
>
>
> On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <
> [hidden email]> wrote:
>
>> Hi Geology Guy, possibly geologists think different.
>>
>> There are gray or color images with bright background and others with a
>> dark background. This should not be mixed up with the representation of
>> binary images. Foreground is always the set of pixels which are thresholded
>> (shown with the small box) in the histogram of the interactive thresholding
>> window. They get a value of 255. The background gets 0. Still by the
>> Options->Colors… you can select the representation of foreground and
>> background pixels.
>>
>> Maybe some clarification for you?
>>
>> Karsten
>>
>> (I have to confess that I rarely read manuals, I prefer trial and error)
>>
>> Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]<http://user/SendEmail.jtp?type=node&node=5003767&i=0>>:
>>
>>
>>> Dear Karsten,
>>> Thanks for your response. I checked the Edit> Options> Colors and the
>>> background is black while the Foreground is White. This is what I expect
>>> because after reading the Image J manual, I learnt that Image J only
>> makes
>>> calculations from binary images when the background is black and the
>>> foreground is white.
>>>
>>> I am using the default thresholding (i.e. AUTO) and checked the DARK
>>> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box
>>> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
>>> BACKGROUND". Again this setting that I am using is because the Image J
>>> manual recommended a background that is black and white foreground in
>> order
>>> to be able to carry out calculations involving binary imaging. Or am I
>> wrong
>>> somewhere maybe that's why the background pixels are getting picked up
>> in
>>> the foreground when I try to calculate Area for foreground objects ONLY?
>>> Thanks for your help.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> Karsten
>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5003767&i=1>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>> ------------------------------
>> If you reply to this email, your message will be added to the discussion
>> below:
>>
>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003767.html
>> To unsubscribe from Isolating the background pixels from foreground
>> pixels, click here<
>> .
>> NAML<
http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>
>
>
> W06.08_20 ParticleData.xls (50K) <http://imagej.1557.x6.nabble.com/attachment/5004170/0/W06.08_20%20ParticleData.xls>
> W06.08_20 Summary of Particle Data.xls (446 bytes) <http://imagej.1557.x6.nabble.com/attachment/5004170/1/W06.08_20%20Summary%20of%20Particle%20Data.xls>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004170.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Karsten
[hidden email]

--
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Re: Isolating the background pixels from foreground pixels

Geology Guy
Dear Karsten,
It was more of my Professor's choice for me to collect all the data regardless of whether I need it or not, but I will focus on the ones you have suggested for now. I thank you very much for responding on time and I hope you have a great day.


On Sat, Jul 27, 2013 at 6:40 AM, Karsten Rodenacker-3 [via ImageJ] <[hidden email]> wrote:
Hi Geology Guy,

Seemingly you have switched on all features. For the shape of particles there are IMHO only senseful:

Area (*)
Perimeter (*)
Circ (*)
Solidity (*)
Round (*)
Feret (*)
MinFeret
Minor/Major

all others are related to redirection to gray scale image or not really helpful for particle shape description, better for representation e.g. by ellipsoids.

To summarize a set of particles:

The features (*) can be summarized by the usual Mean and SD.
 
Min Feret is special, either the (global) Minimum or the span (Max-Min) could characterize the set os particles.

Feret Angle and Angle might be helpful for elongated particles, but the mean of angles is a difficult task since angles come from a number module. (to difficult for the available time!)

The mean of (Minor/Major), a ratio estimator is mean(Minor)/mean(Major) not mean(Minor/Major). SD of the ratio is a bit complicated too!

I think this list of features should be enough for characterization of a set of particles!

Hope that helps a bit

Regards
Karsten

Am 27.07.2013 um 03:47 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
>
> I am trying to measure the parameters of 100 particles in Image J and under

> "Analyze Particles", I also selected the "Summary option". My main problem
> now is that I deleted some of the particles as requested by my Professor
> from the list after the data was provided by Image J. This makes the
> "Summary" data not useful anymore as they do not reflect all the 100
> particles I started with originally. I measured all the parameters under
> "Set measurement" for each particle so now I need to produce a new summary
> data as the values would be used in plotting graphs. I have figured out how
> to Area which is just a simple addition of the areas of each particle.
> Other parameters that are in the summary that I cannot determine from the
> particles data are the following:
>
>
>
>
>
>
>
> Perim.
>
> Major
>
> Minor
>
> Circ.
>
> Solidity
>
> Feret
>
> FeretX
>
> FeretY
>
> FeretAngle
>
> MinFeret
>
> IntDen
>
> Median
>
> Skew
>
> Kurt
>
>
>
> I have attached 2 Excel spreadsheets. The first shows my original particles
> data and the highlighted rows in yellow are rows that I have deleted their
> data as they are bad data. I am working on my research that is due on the
> 31st of this month so this is very urgent. Thank you very much for your
> assistance.
>
>
> Yours faithfully,
>
> Tola
>
>
> On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <
> [hidden email]> wrote:

>
>> Hi Geology Guy, possibly geologists think different.
>>
>> There are gray or color images with bright background and others with a
>> dark background. This should not be mixed up with the representation of
>> binary images. Foreground is always the set of pixels which are thresholded
>> (shown with the small box) in the histogram of the interactive thresholding
>> window. They get a value of 255. The background gets 0. Still by the
>> Options->Colors… you can select the representation of foreground and
>> background pixels.
>>
>> Maybe some clarification for you?
>>
>> Karsten
>>
>> (I have to confess that I rarely read manuals, I prefer trial and error)
>>
>> Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]<http://user/SendEmail.jtp?type=node&node=5003767&i=0>>:
>>

>>
>>> Dear Karsten,
>>> Thanks for your response. I checked the Edit> Options> Colors and the
>>> background is black while the Foreground is White. This is what I expect
>>> because after reading the Image J manual, I learnt that Image J only
>> makes
>>> calculations from binary images when the background is black and the
>>> foreground is white.
>>>
>>> I am using the default thresholding (i.e. AUTO) and checked the DARK
>>> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box
>>> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
>>> BACKGROUND". Again this setting that I am using is because the Image J
>>> manual recommended a background that is black and white foreground in
>> order
>>> to be able to carry out calculations involving binary imaging. Or am I
>> wrong
>>> somewhere maybe that's why the background pixels are getting picked up
>> in
>>> the foreground when I try to calculate Area for foreground objects ONLY?
>>> Thanks for your help.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> Karsten
>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5003767&i=1>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>> ------------------------------
Karsten
[hidden email]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html



If you reply to this email, your message will be added to the discussion below:
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Re: Isolating the background pixels from foreground pixels

Geology Guy
In reply to this post by karo03
Dear Karsten,
I was having a look at the Shape descriptor values that I got for the images that I processed and found out that the value for Aspect Ratio was above 1. So in the particle summary Circ and Solidity were reported but not Aspect ratio and Roundness (Round). Is this because I did a bit of thresholding and water shed segmentation on the image or do you can you tell me the cause of these high values?

Thank you


On Sat, Jul 27, 2013 at 7:23 AM, Tola Ogunniyi <[hidden email]> wrote:
Dear Karsten,
It was more of my Professor's choice for me to collect all the data regardless of whether I need it or not, but I will focus on the ones you have suggested for now. I thank you very much for responding on time and I hope you have a great day.


On Sat, Jul 27, 2013 at 6:40 AM, Karsten Rodenacker-3 [via ImageJ] <[hidden email]> wrote:
Hi Geology Guy,

Seemingly you have switched on all features. For the shape of particles there are IMHO only senseful:

Area (*)
Perimeter (*)
Circ (*)
Solidity (*)
Round (*)
Feret (*)
MinFeret
Minor/Major

all others are related to redirection to gray scale image or not really helpful for particle shape description, better for representation e.g. by ellipsoids.

To summarize a set of particles:

The features (*) can be summarized by the usual Mean and SD.
 
Min Feret is special, either the (global) Minimum or the span (Max-Min) could characterize the set os particles.

Feret Angle and Angle might be helpful for elongated particles, but the mean of angles is a difficult task since angles come from a number module. (to difficult for the available time!)

The mean of (Minor/Major), a ratio estimator is mean(Minor)/mean(Major) not mean(Minor/Major). SD of the ratio is a bit complicated too!

I think this list of features should be enough for characterization of a set of particles!

Hope that helps a bit

Regards
Karsten

Am 27.07.2013 um 03:47 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
>
> I am trying to measure the parameters of 100 particles in Image J and under

> "Analyze Particles", I also selected the "Summary option". My main problem
> now is that I deleted some of the particles as requested by my Professor
> from the list after the data was provided by Image J. This makes the
> "Summary" data not useful anymore as they do not reflect all the 100
> particles I started with originally. I measured all the parameters under
> "Set measurement" for each particle so now I need to produce a new summary
> data as the values would be used in plotting graphs. I have figured out how
> to Area which is just a simple addition of the areas of each particle.
> Other parameters that are in the summary that I cannot determine from the
> particles data are the following:
>
>
>
>
>
>
>
> Perim.
>
> Major
>
> Minor
>
> Circ.
>
> Solidity
>
> Feret
>
> FeretX
>
> FeretY
>
> FeretAngle
>
> MinFeret
>
> IntDen
>
> Median
>
> Skew
>
> Kurt
>
>
>
> I have attached 2 Excel spreadsheets. The first shows my original particles
> data and the highlighted rows in yellow are rows that I have deleted their
> data as they are bad data. I am working on my research that is due on the
> 31st of this month so this is very urgent. Thank you very much for your
> assistance.
>
>
> Yours faithfully,
>
> Tola
>
>
> On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <
> [hidden email]> wrote:

>
>> Hi Geology Guy, possibly geologists think different.
>>
>> There are gray or color images with bright background and others with a
>> dark background. This should not be mixed up with the representation of
>> binary images. Foreground is always the set of pixels which are thresholded
>> (shown with the small box) in the histogram of the interactive thresholding
>> window. They get a value of 255. The background gets 0. Still by the
>> Options->Colors… you can select the representation of foreground and
>> background pixels.
>>
>> Maybe some clarification for you?
>>
>> Karsten
>>
>> (I have to confess that I rarely read manuals, I prefer trial and error)
>>
>> Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]<http://user/SendEmail.jtp?type=node&node=5003767&i=0>>:
>>

>>
>>> Dear Karsten,
>>> Thanks for your response. I checked the Edit> Options> Colors and the
>>> background is black while the Foreground is White. This is what I expect
>>> because after reading the Image J manual, I learnt that Image J only
>> makes
>>> calculations from binary images when the background is black and the
>>> foreground is white.
>>>
>>> I am using the default thresholding (i.e. AUTO) and checked the DARK
>>> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue box
>>> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
>>> BACKGROUND". Again this setting that I am using is because the Image J
>>> manual recommended a background that is black and white foreground in
>> order
>>> to be able to carry out calculations involving binary imaging. Or am I
>> wrong
>>> somewhere maybe that's why the background pixels are getting picked up
>> in
>>> the foreground when I try to calculate Area for foreground objects ONLY?
>>> Thanks for your help.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> Karsten
>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5003767&i=1>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>> ------------------------------
>> If you reply to this email, your message will be added to the discussion
>> below:
>>
>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003767.html
>> To unsubscribe from Isolating the background pixels from foreground

>> pixels, click here<

>> .
>> NAML<
http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>
>
>
> W06.08_20 ParticleData.xls (50K) <http://imagej.1557.x6.nabble.com/attachment/5004170/0/W06.08_20%20ParticleData.xls>
> W06.08_20 Summary of Particle Data.xls (446 bytes) <http://imagej.1557.x6.nabble.com/attachment/5004170/1/W06.08_20%20Summary%20of%20Particle%20Data.xls>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004170.html

> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Karsten
[hidden email]

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Re: Isolating the background pixels from foreground pixels

karo03
AR in ImageJ is calculated as Major/Minor. I prefer the inverse as number ]0,1] instead of [1,…[ .

Concerning summary of AR and Round, I don't know. If they are set in "Set Measurements" they should appear as columns in the results table independent on mask treatment (run("Set Measurements…", "area centroid center perimeter bounding fit shape ferret's area_fraction display redirect=None decimal=3");). And hence would appear in the summary lines.

Karsten
 
Am 30.07.2013 um 04:31 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
> I was having a look at the Shape descriptor values that I got for the
> images that I processed and found out that the value for Aspect Ratio was
> above 1. So in the particle summary Circ and Solidity were reported but not
> Aspect ratio and Roundness (Round). Is this because I did a bit of
> thresholding and water shed segmentation on the image or do you can you
> tell me the cause of these high values?
>
> Thank you
>
>
> On Sat, Jul 27, 2013 at 7:23 AM, Tola Ogunniyi <[hidden email]> wrote:
>
>> Dear Karsten,
>> It was more of my Professor's choice for me to collect all the data
>> regardless of whether I need it or not, but I will focus on the ones you
>> have suggested for now. I thank you very much for responding on time and I
>> hope you have a great day.
>>
>>
>> On Sat, Jul 27, 2013 at 6:40 AM, Karsten Rodenacker-3 [via ImageJ] <
>> [hidden email]> wrote:
>>
>>> Hi Geology Guy,
>>>
>>> Seemingly you have switched on all features. For the shape of particles
>>> there are IMHO only senseful:
>>>
>>> Area (*)
>>> Perimeter (*)
>>> Circ (*)
>>> Solidity (*)
>>> Round (*)
>>> Feret (*)
>>> MinFeret
>>> Minor/Major
>>>
>>> all others are related to redirection to gray scale image or not really
>>> helpful for particle shape description, better for representation e.g. by
>>> ellipsoids.
>>>
>>> To summarize a set of particles:
>>>
>>> The features (*) can be summarized by the usual Mean and SD.
>>>
>>> Min Feret is special, either the (global) Minimum or the span (Max-Min)
>>> could characterize the set os particles.
>>>
>>> Feret Angle and Angle might be helpful for elongated particles, but the
>>> mean of angles is a difficult task since angles come from a number module.
>>> (to difficult for the available time!)
>>>
>>> The mean of (Minor/Major), a ratio estimator is mean(Minor)/mean(Major)
>>> not mean(Minor/Major). SD of the ratio is a bit complicated too!
>>>
>>> I think this list of features should be enough for characterization of a
>>> set of particles!
>>>
>>> Hope that helps a bit
>>>
>>> Regards
>>> Karsten
>>>
>>> Am 27.07.2013 um 03:47 schrieb Geology Guy <[hidden email]<http://user/SendEmail.jtp?type=node&node=5004175&i=0>>:
>>>
>>>
>>>> Dear Karsten,
>>>>
>>>> I am trying to measure the parameters of 100 particles in Image J and
>>> under
>>>> "Analyze Particles", I also selected the "Summary option". My main
>>> problem
>>>> now is that I deleted some of the particles as requested by my
>>> Professor
>>>> from the list after the data was provided by Image J. This makes the
>>>> "Summary" data not useful anymore as they do not reflect all the 100
>>>> particles I started with originally. I measured all the parameters
>>> under
>>>> "Set measurement" for each particle so now I need to produce a new
>>> summary
>>>> data as the values would be used in plotting graphs. I have figured out
>>> how
>>>> to Area which is just a simple addition of the areas of each particle.
>>>> Other parameters that are in the summary that I cannot determine from
>>> the
>>>> particles data are the following:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Perim.
>>>>
>>>> Major
>>>>
>>>> Minor
>>>>
>>>> Circ.
>>>>
>>>> Solidity
>>>>
>>>> Feret
>>>>
>>>> FeretX
>>>>
>>>> FeretY
>>>>
>>>> FeretAngle
>>>>
>>>> MinFeret
>>>>
>>>> IntDen
>>>>
>>>> Median
>>>>
>>>> Skew
>>>>
>>>> Kurt
>>>>
>>>>
>>>>
>>>> I have attached 2 Excel spreadsheets. The first shows my original
>>> particles
>>>> data and the highlighted rows in yellow are rows that I have deleted
>>> their
>>>> data as they are bad data. I am working on my research that is due on
>>> the
>>>> 31st of this month so this is very urgent. Thank you very much for your
>>>> assistance.
>>>>
>>>>
>>>> Yours faithfully,
>>>>
>>>> Tola
>>>>
>>>>
>>>> On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <
>>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5004175&i=1>>
>>> wrote:
>>>>
>>>>> Hi Geology Guy, possibly geologists think different.
>>>>>
>>>>> There are gray or color images with bright background and others with
>>> a
>>>>> dark background. This should not be mixed up with the representation
>>> of
>>>>> binary images. Foreground is always the set of pixels which are
>>> thresholded
>>>>> (shown with the small box) in the histogram of the interactive
>>> thresholding
>>>>> window. They get a value of 255. The background gets 0. Still by the
>>>>> Options->Colors… you can select the representation of foreground and
>>>>> background pixels.
>>>>>
>>>>> Maybe some clarification for you?
>>>>>
>>>>> Karsten
>>>>>
>>>>> (I have to confess that I rarely read manuals, I prefer trial and
>>> error)
>>>>>
>>>>> Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]<
>>> http://user/SendEmail.jtp?type=node&node=5003767&i=0>>:
>>>>>
>>>>>
>>>>>> Dear Karsten,
>>>>>> Thanks for your response. I checked the Edit> Options> Colors and the
>>>>>> background is black while the Foreground is White. This is what I
>>> expect
>>>>>> because after reading the Image J manual, I learnt that Image J only
>>>>> makes
>>>>>> calculations from binary images when the background is black and the
>>>>>> foreground is white.
>>>>>>
>>>>>> I am using the default thresholding (i.e. AUTO) and checked the DARK
>>>>>> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue
>>> box
>>>>>> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
>>>>>> BACKGROUND". Again this setting that I am using is because the Image
>>> J
>>>>>> manual recommended a background that is black and white foreground in
>>>>> order
>>>>>> to be able to carry out calculations involving binary imaging. Or am
>>> I
>>>>> wrong
>>>>>> somewhere maybe that's why the background pixels are getting picked
>>> up
>>>>> in
>>>>>> the foreground when I try to calculate Area for foreground objects
>>> ONLY?
>>>>>> Thanks for your help.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> View this message in context:
>>>>>
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
>>>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>> Karsten
>>>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5003767&i=1>
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>>
>>>>> ------------------------------
>>>>> If you reply to this email, your message will be added to the
>>> discussion
>>>>> below:
>>>>>
>>>>>
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003767.html
>>>>> To unsubscribe from Isolating the background pixels from foreground
>>>>> pixels, click here<
>>>
>>>>> .
>>>>> NAML<
>>> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>
>>>>>
>>>>
>>>>
>>>> W06.08_20 ParticleData.xls (50K) <
>>> http://imagej.1557.x6.nabble.com/attachment/5004170/0/W06.08_20%20ParticleData.xls>
>>>
>>>> W06.08_20 Summary of Particle Data.xls (446 bytes) <
>>> http://imagej.1557.x6.nabble.com/attachment/5004170/1/W06.08_20%20Summary%20of%20Particle%20Data.xls>
>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004170.html
>>>
>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> Karsten
>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5004175&i=2>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>>
>>> ------------------------------
>>> If you reply to this email, your message will be added to the
>>> discussion below:
>>>
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004175.html
>>> To unsubscribe from Isolating the background pixels from foreground
>>> pixels, click here<
>>> .
>>> NAML<
http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>
>>
>>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004207.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Karsten
[hidden email]

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Re: Isolating the background pixels from foreground pixels

Geology Guy
Dear Karsten,
I will talk to my Professor about it and see what he says. Thank you very much


On Tue, Jul 30, 2013 at 3:07 AM, Karsten Rodenacker-3 [via ImageJ] <[hidden email]> wrote:
AR in ImageJ is calculated as Major/Minor. I prefer the inverse as number ]0,1] instead of [1,…[ .

Concerning summary of AR and Round, I don't know. If they are set in "Set Measurements" they should appear as columns in the results table independent on mask treatment (run("Set Measurements…", "area centroid center perimeter bounding fit shape ferret's area_fraction display redirect=None decimal=3");). And hence would appear in the summary lines.

Karsten
 
Am 30.07.2013 um 04:31 schrieb Geology Guy <[hidden email]>:

> Dear Karsten,
> I was having a look at the Shape descriptor values that I got for the
> images that I processed and found out that the value for Aspect Ratio was
> above 1. So in the particle summary Circ and Solidity were reported but not
> Aspect ratio and Roundness (Round). Is this because I did a bit of
> thresholding and water shed segmentation on the image or do you can you
> tell me the cause of these high values?
>
> Thank you
>
>
> On Sat, Jul 27, 2013 at 7:23 AM, Tola Ogunniyi <[hidden email]> wrote:
>
>> Dear Karsten,
>> It was more of my Professor's choice for me to collect all the data
>> regardless of whether I need it or not, but I will focus on the ones you
>> have suggested for now. I thank you very much for responding on time and I
>> hope you have a great day.
>>
>>
>> On Sat, Jul 27, 2013 at 6:40 AM, Karsten Rodenacker-3 [via ImageJ] <
>> [hidden email]> wrote:
>>
>>> Hi Geology Guy,
>>>
>>> Seemingly you have switched on all features. For the shape of particles

>>> there are IMHO only senseful:
>>>
>>> Area (*)
>>> Perimeter (*)
>>> Circ (*)
>>> Solidity (*)
>>> Round (*)
>>> Feret (*)
>>> MinFeret
>>> Minor/Major
>>>
>>> all others are related to redirection to gray scale image or not really
>>> helpful for particle shape description, better for representation e.g. by
>>> ellipsoids.
>>>
>>> To summarize a set of particles:
>>>
>>> The features (*) can be summarized by the usual Mean and SD.
>>>
>>> Min Feret is special, either the (global) Minimum or the span (Max-Min)
>>> could characterize the set os particles.
>>>
>>> Feret Angle and Angle might be helpful for elongated particles, but the
>>> mean of angles is a difficult task since angles come from a number module.
>>> (to difficult for the available time!)
>>>
>>> The mean of (Minor/Major), a ratio estimator is mean(Minor)/mean(Major)
>>> not mean(Minor/Major). SD of the ratio is a bit complicated too!
>>>
>>> I think this list of features should be enough for characterization of a
>>> set of particles!
>>>
>>> Hope that helps a bit
>>>
>>> Regards
>>> Karsten
>>>
>>> Am 27.07.2013 um 03:47 schrieb Geology Guy <[hidden email]<http://user/SendEmail.jtp?type=node&node=5004175&i=0>>:
>>>

>>>
>>>> Dear Karsten,
>>>>
>>>> I am trying to measure the parameters of 100 particles in Image J and
>>> under
>>>> "Analyze Particles", I also selected the "Summary option". My main
>>> problem
>>>> now is that I deleted some of the particles as requested by my
>>> Professor
>>>> from the list after the data was provided by Image J. This makes the
>>>> "Summary" data not useful anymore as they do not reflect all the 100
>>>> particles I started with originally. I measured all the parameters
>>> under
>>>> "Set measurement" for each particle so now I need to produce a new
>>> summary
>>>> data as the values would be used in plotting graphs. I have figured out
>>> how
>>>> to Area which is just a simple addition of the areas of each particle.
>>>> Other parameters that are in the summary that I cannot determine from
>>> the
>>>> particles data are the following:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Perim.
>>>>
>>>> Major
>>>>
>>>> Minor
>>>>
>>>> Circ.
>>>>
>>>> Solidity
>>>>
>>>> Feret
>>>>
>>>> FeretX
>>>>
>>>> FeretY
>>>>
>>>> FeretAngle
>>>>
>>>> MinFeret
>>>>
>>>> IntDen
>>>>
>>>> Median
>>>>
>>>> Skew
>>>>
>>>> Kurt
>>>>
>>>>
>>>>
>>>> I have attached 2 Excel spreadsheets. The first shows my original
>>> particles
>>>> data and the highlighted rows in yellow are rows that I have deleted
>>> their
>>>> data as they are bad data. I am working on my research that is due on
>>> the
>>>> 31st of this month so this is very urgent. Thank you very much for your
>>>> assistance.
>>>>
>>>>
>>>> Yours faithfully,
>>>>
>>>> Tola
>>>>
>>>>
>>>> On Thu, Jul 4, 2013 at 5:10 PM, Karsten Rodenacker-3 [via ImageJ] <
>>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5004175&i=1>>
>>> wrote:

>>>>
>>>>> Hi Geology Guy, possibly geologists think different.
>>>>>
>>>>> There are gray or color images with bright background and others with
>>> a
>>>>> dark background. This should not be mixed up with the representation
>>> of
>>>>> binary images. Foreground is always the set of pixels which are
>>> thresholded
>>>>> (shown with the small box) in the histogram of the interactive
>>> thresholding
>>>>> window. They get a value of 255. The background gets 0. Still by the
>>>>> Options->Colors… you can select the representation of foreground and
>>>>> background pixels.
>>>>>
>>>>> Maybe some clarification for you?
>>>>>
>>>>> Karsten
>>>>>
>>>>> (I have to confess that I rarely read manuals, I prefer trial and
>>> error)
>>>>>
>>>>> Am 04.07.2013 um 22:49 schrieb Geology Guy <[hidden email]<
>>> http://user/SendEmail.jtp?type=node&node=5003767&i=0>>:
>>>>>
>>>>>
>>>>>> Dear Karsten,
>>>>>> Thanks for your response. I checked the Edit> Options> Colors and the
>>>>>> background is black while the Foreground is White. This is what I
>>> expect
>>>>>> because after reading the Image J manual, I learnt that Image J only
>>>>> makes
>>>>>> calculations from binary images when the background is black and the
>>>>>> foreground is white.
>>>>>>
>>>>>> I am using the default thresholding (i.e. AUTO) and checked the DARK
>>>>>> BACKGROUND BOX. Then when I was ready to do binary image a,dialogue
>>> box
>>>>>> popped up and I unchecked the box next to "BLACK FOREGROUND and WHITE
>>>>>> BACKGROUND". Again this setting that I am using is because the Image
>>> J
>>>>>> manual recommended a background that is black and white foreground in
>>>>> order
>>>>>> to be able to carry out calculations involving binary imaging. Or am
>>> I
>>>>> wrong
>>>>>> somewhere maybe that's why the background pixels are getting picked
>>> up
>>>>> in
>>>>>> the foreground when I try to calculate Area for foreground objects
>>> ONLY?
>>>>>> Thanks for your help.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> View this message in context:
>>>>>
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003766.html
>>>>>> Sent from the ImageJ mailing list archive at Nabble.com.

>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>> Karsten
>>>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5003767&i=1>
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>>
>>>>> ------------------------------
>>>>> If you reply to this email, your message will be added to the
>>> discussion
>>>>> below:
>>>>>
>>>>>
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5003767.html
>>>>> To unsubscribe from Isolating the background pixels from foreground >>>
>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>> Karsten
>>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5004175&i=2>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>>
>>> ------------------------------
>>> If you reply to this email, your message will be added to the
>>> discussion below:
>>>
>>> http://imagej.1557.x6.nabble.com/Isolating-the-background-pixels-from-foreground-pixels-tp5003764p5004175.html
>>> To unsubscribe from Isolating the background pixels from foreground
>>> pixels, click here<
Karsten
[hidden email]

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