Integrated Density Unit help? please

[Kashif Zeeshan]

HI experts,

 

I need some help about Integrated Density. My scale is in µm. Now I want to
know what will be the unit of Integrated Density? For Area, it is µm2 and
for Feret’s Diameter µm and for circularity, no unit at all. Can you kindly
help me in this regard?

 

Cordially.

 

Kashif ZEESHAN

(00 33 6 74 90 18 10)

Doctorant, Biopesticide Group,

Laboratoire Universitaire de

Biodiversité et d'Ecologie

Microbienne (LUBEM),

6 Rue de l'Université,

29334, Quimper Cedex,

France

 

[Thomas Boudier]

Hi Kashif,

Maybe you should have a look to the documentation ;-) , Integrated
density is the sum of pixel values inside the object, it is not a
geometrical measure like area or volume.

Thomas

> HI experts
>  
>
> I need some help about Integrated Density. My scale is in µm. Now I want to
> know what will be the unit of Integrated Density? For Area, it is µm2 and
> for Feret’s Diameter µm and for circularity, no unit at all. Can you kindly
> help me in this regard?
>
>  
>
> Cordially.
>
>  
>
> Kashif ZEESHAN
>
> (00 33 6 74 90 18 10)
>
> Doctorant, Biopesticide Group,
>
> Laboratoire Universitaire de
>
> Biodiversité et d'Ecologie
>
> Microbienne (LUBEM),
>
> 6 Rue de l'Université,
>
> 29334, Quimper Cedex,
>
> France
>
>  
>
>
>  

--
/*****************************************************/
   Thomas Boudier, MCU Université Paris 6,
   UMR 7101 / IFR 83. Bat A 328, Jussieu.
   Tel : [phone]  Fax : [phone]
/****************************************************/

[Kashif Zeeshan]

Thanks for reply. I have read the documentation about integrated density.
There it is said that it is sum of pixels values inside the object but I
scaled pixels as µm and there is written also that it is equal to the
product of area and mean gray values. That’s why I was confused about the
unit. Because all the images used are the scaled images. Should I consider
this integrated density without unit in my case or should I consider it as
pixels which are µm in my case. I hope that I was a little bit clear in my
question.

Cordially.

Kashif ZEESHAN
(00 33 6 74 90 18 10)
Doctorant, Biopesticide Group,
Laboratoire Universitaire de
Biodiversité et d'Ecologie
Microbienne (LUBEM),
6 Rue de l'Université,
29334, Quimper Cedex,
France
-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Thomas
Boudier
Envoyé : jeudi 19 juin 2008 16:23
À : [hidden email]
Objet : Re: Integrated Density Unit help? please

Hi Kashif,

Maybe you should have a look to the documentation ;-) , Integrated
density is the sum of pixel values inside the object, it is not a
geometrical measure like area or volume.

Thomas

> HI experts
>  
>
> I need some help about Integrated Density. My scale is in µm. Now I want
to
> know what will be the unit of Integrated Density? For Area, it is µm2 and
> for Feret’s Diameter µm and for circularity, no unit at all. Can you
kindly

> help me in this regard?
>
>  
>
> Cordially.
>
>  
>
> Kashif ZEESHAN
>
> (00 33 6 74 90 18 10)
>
> Doctorant, Biopesticide Group,
>
> Laboratoire Universitaire de
>
> Biodiversité et d'Ecologie
>
> Microbienne (LUBEM),
>
> 6 Rue de l'Université,
>
> 29334, Quimper Cedex,
>
> France
>
>  
>
>
>  

--
/*****************************************************/
   Thomas Boudier, MCU Université Paris 6,
   UMR 7101 / IFR 83. Bat A 328, Jussieu.
   Tel : [phone]  Fax : [phone]
/****************************************************/

[Thomas Boudier]

ok I understand your trouble. The area here corresponds to the number of
pixels and does not take into account the spatial calibration. So the
integrated density has the unit of pixel values, that is to say gray
levels.

Thomas

> Thanks for reply. I have read the documentation about integrated density.
> There it is said that it is sum of pixels values inside the object but I
> scaled pixels as µm and there is written also that it is equal to the
> product of area and mean gray values. That’s why I was confused about the
> unit. Because all the images used are the scaled images. Should I consider
> this integrated density without unit in my case or should I consider it as
> pixels which are µm in my case. I hope that I was a little bit clear in my
> question.
>
> Cordially.
>
> Kashif ZEESHAN
> (00 33 6 74 90 18 10)
> Doctorant, Biopesticide Group,
> Laboratoire Universitaire de
> Biodiversité et d'Ecologie
> Microbienne (LUBEM),
> 6 Rue de l'Université,
> 29334, Quimper Cedex,
> France
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de Thomas
> Boudier
> Envoyé : jeudi 19 juin 2008 16:23
> À : [hidden email]
> Objet : Re: Integrated Density Unit help? please
>
> Hi Kashif,
>
> Maybe you should have a look to the documentation ;-) , Integrated
> density is the sum of pixel values inside the object, it is not a
> geometrical measure like area or volume.
>
> Thomas
>
>  
>> HI experts
>>  
>>
>> I need some help about Integrated Density. My scale is in µm. Now I want
>>    
> to
>  
>> know what will be the unit of Integrated Density? For Area, it is µm2 and
>> for Feret’s Diameter µm and for circularity, no unit at all. Can you
>>    
> kindly
>  
>> help me in this regard?
>>
>>  
>>
>> Cordially.
>>
>>  
>>
>> Kashif ZEESHAN
>>
>> (00 33 6 74 90 18 10)
>>
>> Doctorant, Biopesticide Group,
>>
>> Laboratoire Universitaire de
>>
>> Biodiversité et d'Ecologie
>>
>> Microbienne (LUBEM),
>>
>> 6 Rue de l'Université,
>>
>> 29334, Quimper Cedex,
>>
>> France
>>
>>  
>>
>>
>>  
>>    
>
>
>  

--
/*****************************************************/
   Thomas Boudier, MCU Université Paris 6,
   UMR 7101 / IFR 83. Bat A 328, Jussieu.
   Tel : [phone]  Fax : [phone]
/****************************************************/

[lechristophe]

This is indeed a quite tricky question, see the previous discussion
some time ago on this list :
http://www.nabble.com/Integrated-Density-and-Image-Scale-td16402023.html

It appears that the ID measurement takes into account the image
spatial scale (if you change the scale of an image and measure it
again, your ID values change accordingly). I still don't understand
why (it is contradictory to the definition of ID given in the ImageJ
doc), but it seems to be valid.

I ended up systematically resetting the scale of all images before
processing in my macros to avoid having problems with files that are
imported with or without scaling information...

Christophe

On Thu, Jun 19, 2008 at 17:29, Thomas Boudier
<[hidden email]> wrote:

> ok I understand your trouble. The area here corresponds to the number of
> pixels and does not take into account the spatial calibration. So the
> integrated density has the unit of pixel values, that is to say gray levels.
>
> Thomas
>
>> Thanks for reply. I have read the documentation about integrated density.
>> There it is said that it is sum of pixels values inside the object but I
>> scaled pixels as µm and there is written also that it is equal to the
>> product of area and mean gray values. That's why I was confused about the
>> unit. Because all the images used are the scaled images. Should I consider
>> this integrated density without unit in my case or should I consider it as
>> pixels which are µm in my case. I hope that I was a little bit clear in my
>> question.
>>
>> Cordially.
>>
>> Kashif ZEESHAN
>> (00 33 6 74 90 18 10)
>> Doctorant, Biopesticide Group,
>> Laboratoire Universitaire de
>> Biodiversité et d'Ecologie Microbienne (LUBEM),
>> 6 Rue de l'Université,
>> 29334, Quimper Cedex,
>> France
>> -----Message d'origine-----
>> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
>> Thomas
>> Boudier
>> Envoyé : jeudi 19 juin 2008 16:23
>> À : [hidden email]
>> Objet : Re: Integrated Density Unit help? please
>>
>> Hi Kashif,
>>
>> Maybe you should have a look to the documentation ;-) , Integrated density
>> is the sum of pixel values inside the object, it is not a geometrical
>> measure like area or volume.
>>
>> Thomas
>>
>>
>>>
>>> HI experts
>>>
>>> I need some help about Integrated Density. My scale is in µm. Now I want
>>>
>>
>> to
>>
>>>
>>> know what will be the unit of Integrated Density? For Area, it is µm2 and
>>> for Feret's Diameter µm and for circularity, no unit at all. Can you
>>>
>>
>> kindly
>>
>>>
>>> help me in this regard?
>>>
>>>
>>> Cordially.
>>>
>>>
>>> Kashif ZEESHAN
>>>
>>> (00 33 6 74 90 18 10)
>>>
>>> Doctorant, Biopesticide Group,
>>>
>>> Laboratoire Universitaire de
>>>
>>> Biodiversité et d'Ecologie
>>> Microbienne (LUBEM),
>>>
>>> 6 Rue de l'Université,
>>>
>>> 29334, Quimper Cedex,
>>>
>>> France
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
> --
> /*****************************************************/
>  Thomas Boudier, MCU Université Paris 6,
>  UMR 7101 / IFR 83. Bat A 328, Jussieu.
>  Tel : [phone]  Fax : [phone]
> /****************************************************/
>

[David Randell]

Hi everybody,

Does anyone have a plugin/macro that computes the exact Euclidean Distance
Map?  I have been looking at the one shipped with ImageJ which for propogated
wavefront distances greater than 25 pixels or so, visibly departs from the
ideal circular wavefront and tends toward a 16-sided regular polygon.

Many thanks,
Dave Randell

[Robert Dougherty]

Dave,

You might try the 3D software at http://www.optinav.com/Local_Thickness.htm.
It is intended to work in 2D as well.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> David Randell
> Sent: Friday, June 20, 2008 9:57 AM
> To: [hidden email]
> Subject: exact EDM algorithm
>
> Hi everybody,
>
> Does anyone have a plugin/macro that computes the exact Euclidean Distance
> Map?  I have been looking at the one shipped with ImageJ which for
> propogated
> wavefront distances greater than 25 pixels or so, visibly departs from the
> ideal circular wavefront and tends toward a 16-sided regular polygon.
>
> Many thanks,
> Dave Randell

[Kashif Zeeshan]

Thanks every body for your nice help. Now I understood (if I well
understood) that in my case, the unit for integrated density will be micron
square as the images are scaled in microns. Now I have another question
please. May be it is really very easy to know this but I was wondering that
how can I be able to say that which aggregate is very dense, average dense
and less dense? As I want to make three groups of the aggregates according
to aggregates so that in the end I can compare different aggregates from
different conditions. Can you kindly give me some suggestions/information in
this regard?

Thanks again.

Kashif ZEESHAN
(00 33 6 74 90 18 10)
Doctorant, Biopesticide Group,
Laboratoire Universitaire de
Biodiversité et d'Ecologie
Microbienne (LUBEM),
6 Rue de l'Université,
29334, Quimper Cedex,
France
-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de
Christophe Leterrier
Envoyé : jeudi 19 juin 2008 23:36
À : [hidden email]
Objet : Re: Integrated Density Unit help? please

This is indeed a quite tricky question, see the previous discussion
some time ago on this list :
http://www.nabble.com/Integrated-Density-and-Image-Scale-td16402023.html

It appears that the ID measurement takes into account the image
spatial scale (if you change the scale of an image and measure it
again, your ID values change accordingly). I still don't understand
why (it is contradictory to the definition of ID given in the ImageJ
doc), but it seems to be valid.

I ended up systematically resetting the scale of all images before
processing in my macros to avoid having problems with files that are
imported with or without scaling information...

Christophe

On Thu, Jun 19, 2008 at 17:29, Thomas Boudier
<[hidden email]> wrote:
> ok I understand your trouble. The area here corresponds to the number of
> pixels and does not take into account the spatial calibration. So the
> integrated density has the unit of pixel values, that is to say gray
levels.
>
> Thomas
>
>> Thanks for reply. I have read the documentation about integrated density.
>> There it is said that it is sum of pixels values inside the object but I
>> scaled pixels as µm and there is written also that it is equal to the
>> product of area and mean gray values. That's why I was confused about the
>> unit. Because all the images used are the scaled images. Should I
consider
>> this integrated density without unit in my case or should I consider it
as
>> pixels which are µm in my case. I hope that I was a little bit clear in
my

>> question.
>>
>> Cordially.
>>
>> Kashif ZEESHAN
>> (00 33 6 74 90 18 10)
>> Doctorant, Biopesticide Group,
>> Laboratoire Universitaire de
>> Biodiversité et d'Ecologie Microbienne (LUBEM),
>> 6 Rue de l'Université,
>> 29334, Quimper Cedex,
>> France
>> -----Message d'origine-----
>> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
>> Thomas
>> Boudier
>> Envoyé : jeudi 19 juin 2008 16:23
>> À : [hidden email]
>> Objet : Re: Integrated Density Unit help? please
>>
>> Hi Kashif,
>>
>> Maybe you should have a look to the documentation ;-) , Integrated

density

>> is the sum of pixel values inside the object, it is not a geometrical
>> measure like area or volume.
>>
>> Thomas
>>
>>
>>>
>>> HI experts
>>>
>>> I need some help about Integrated Density. My scale is in µm. Now I want
>>>
>>
>> to
>>
>>>
>>> know what will be the unit of Integrated Density? For Area, it is µm2

and

>>> for Feret's Diameter µm and for circularity, no unit at all. Can you
>>>
>>
>> kindly
>>
>>>
>>> help me in this regard?
>>>
>>>
>>> Cordially.
>>>
>>>
>>> Kashif ZEESHAN
>>>
>>> (00 33 6 74 90 18 10)
>>>
>>> Doctorant, Biopesticide Group,
>>>
>>> Laboratoire Universitaire de
>>>
>>> Biodiversité et d'Ecologie
>>> Microbienne (LUBEM),
>>>
>>> 6 Rue de l'Université,
>>>
>>> 29334, Quimper Cedex,
>>>
>>> France
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
> --
> /*****************************************************/
>  Thomas Boudier, MCU Université Paris 6,
>  UMR 7101 / IFR 83. Bat A 328, Jussieu.
>  Tel : [phone]  Fax : [phone]
> /****************************************************/
>