Help needed in doing image analysis

[Kashif Zeeshan]

Hello Everybody,

I need your help please. I have a fungus which produce different kinds/forms
of aggregates (pellets, clumps etc) in different media. I am giving a name
“aggregates” to all the forms and my objective is to measure the size/area,
diameter, density etc of all these aggregates. I am in search of a method
which I can use for all of these different forms to do analysis. I mean that
a same analysis method which can be used for all images. I am sending you
the link where I put some of the pictures just to give you an idea how these
aggregates can be. Can you help me in this regard please? If you can guide
me step by step, it will be really very much helpful and I will be very
thankful to all of you. Here is the link.

 

 
<http://s305.photobucket.com/albums/nn227/ablaze212/Images%20for%20Analysis/
>
http://s305.photobucket.com/albums/nn227/ablaze212/Images%20for%20Analysis/

 

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

 

[Sami Badawi-2]

Hi Kashif,

Here is a suggestion:

1: Since your petri dish is always round, you could do a circle
selection inside its edge, in order to avoid the shadows and
highlights on the edge that could be counted as particles.
2: Fill everything outside your circle with the background color
(making it all disappear).
4: Write down the radius or diameter of your circle since this will
give you the area of your dish.
5: Run a particle analyzer on the image.
6: Export the result to an Excel spreadsheet
7: Add circle radius to each spreadsheet for calculating density.

There is a mature particle analyzer coming with ImageJ, it should
probably do what you need based on your images.
There is also a particle analyzer with different properties coming
with the ShapeLogic plugin.

-Sami Badawi
http://www.shapelogic.org


On 8/11/08, Kashif Zeeshan <[hidden email]> wrote:

> Hello Everybody,
>
> I need your help please. I have a fungus which produce different kinds/forms
> of aggregates (pellets, clumps etc) in different media. I am giving a name
> "aggregates" to all the forms and my objective is to measure the size/area,
> diameter, density etc of all these aggregates. I am in search of a method
> which I can use for all of these different forms to do analysis. I mean that
> a same analysis method which can be used for all images. I am sending you
> the link where I put some of the pictures just to give you an idea how these
> aggregates can be. Can you help me in this regard please? If you can guide
> me step by step, it will be really very much helpful and I will be very
> thankful to all of you. Here is the link.
>
>
>
>
> <http://s305.photobucket.com/albums/nn227/ablaze212/Images%20for%20Analysis/
>>
> http://s305.photobucket.com/albums/nn227/ablaze212/Images%20for%20Analysis/
>
>
>
> 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
>
>
>

[Kashif Zeeshan]

Thanks a lot.

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 Sami
Badawi
Envoyé : vendredi 15 août 2008 11:16
À : [hidden email]
Objet : Re: Help needed in doing image analysis

Hi Kashif,

Here is a suggestion:

1: Since your petri dish is always round, you could do a circle
selection inside its edge, in order to avoid the shadows and
highlights on the edge that could be counted as particles.
2: Fill everything outside your circle with the background color
(making it all disappear).
4: Write down the radius or diameter of your circle since this will
give you the area of your dish.
5: Run a particle analyzer on the image.
6: Export the result to an Excel spreadsheet
7: Add circle radius to each spreadsheet for calculating density.

There is a mature particle analyzer coming with ImageJ, it should
probably do what you need based on your images.
There is also a particle analyzer with different properties coming
with the ShapeLogic plugin.

-Sami Badawi
http://www.shapelogic.org


On 8/11/08, Kashif Zeeshan <[hidden email]> wrote:
> Hello Everybody,
>
> I need your help please. I have a fungus which produce different
kinds/forms
> of aggregates (pellets, clumps etc) in different media. I am giving a name
> "aggregates" to all the forms and my objective is to measure the
size/area,
> diameter, density etc of all these aggregates. I am in search of a method
> which I can use for all of these different forms to do analysis. I mean
that
> a same analysis method which can be used for all images. I am sending you
> the link where I put some of the pictures just to give you an idea how
these
> aggregates can be. Can you help me in this regard please? If you can guide
> me step by step, it will be really very much helpful and I will be very
> thankful to all of you. Here is the link.
>
>
>
>
>
<http://s305.photobucket.com/albums/nn227/ablaze212/Images%20for%20Analysis/
>>
>
http://s305.photobucket.com/albums/nn227/ablaze212/Images%20for%20Analysis/

>
>
>
> 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
>
>
>

[Christian Lutz]

Hello,

I am interessted in developing or bug fixing ImageJ and Plugins for  
our biologists.

And so I have some question about the the development process.
- Are there any papers to read?

- Is there a way to access any kind of version control / or is the  
only access via downloading last stable version code?
   ( currently, read access would be enough )

- Are there any manuels for NetBeans? I just found an older one http://www.mbl.edu/research/labs/adlc/CamAcqJ/NetBeansforIJDevelopment.html

- How can I supply patches? To whom?

Thanks and I appricate your help.
Sincerely
Christian

[Albert Cardona]

Hi Christian,


> I am interessted in developing or bug fixing ImageJ and Plugins for
> our biologists.

Always very welcome!


> And so I have some question about the the development process.
> - Are there any papers to read?


Not really. What do you mean by "development process"? To me it means:
test against expectations, fix mismatches.

There is a book on image processing with java and ImageJ on sale on the
web somewhere.
I've written a tutorial here:
http://www.mcdb.ucla.edu/research/hartenstein/acardona/imagej_programming_tutorials.html

There are many more resources at http://imagejdocu.tudor.lu (ImageJ
Documentation Wiki).



> - Is there a way to access any kind of version control / or is the
> only access via downloading last stable version code?
>   ( currently, read access would be enough )


We have setup one: ImageJA at http://repo.or.cz/w/imageja.git/ , which
is perhaps best used as a submodule of fiji  (web:
http://pacific.mpi-cbg.de/   and repository:
http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=summary )



> - Are there any manuels for NetBeans? I just found an older one
> http://www.mbl.edu/research/labs/adlc/CamAcqJ/NetBeansforIJDevelopment.html 
>


At the upcomming ImageJ conference, Volker Baecker will give an in-depth
workshop on how to use Eclipse to develop for ImageJ.
There are also some resources regarding IDE in the ImageJ Documentation
Wiki: http://imagejdocu.tudor.lu


> - How can I supply patches? To whom?


In Fiji, just use the contrib user which needs no password and pushes
only to the contrib branch.
In ImageJA, use the mob user (same status as the contrib user in Fiji).

Some help here:
http://pacific.mpi-cbg.de/wiki/index.php/Git_mini_howto
http://pacific.mpi-cbg.de/wiki/index.php/Git

On the other hand, Wayne preffers fully functional ij.jar, compiled for
java 1.4.2, along with the modified java files in full.



>
> Thanks and I appricate your help.


You are welcome.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Christian Lutz]

Hello Albert,

thank you for the very fast reply!! Great :)



Am 19.08.2008 um 11:51 schrieb Albert Cardona:

> Hi Christian,
>
>
>> I am interessted in developing or bug fixing ImageJ and Plugins for  
>> our biologists.
>
> Always very welcome!
>
>
>> And so I have some question about the the development process.
>> - Are there any papers to read?
>
>
> Not really. What do you mean by "development process"? To me it  
> means: test against expectations, fix mismatches.
>
> There is a book on image processing with java and ImageJ on sale on  
> the web somewhere.

Yes, I lent it, already. But it doesn't help me on that very much.

>
> I've written a tutorial here:
> http://www.mcdb.ucla.edu/research/hartenstein/acardona/imagej_programming_tutorials.html

Thanks.

>
>
> There are many more resources at http://imagejdocu.tudor.lu (ImageJ  
> Documentation Wiki).
>
>
>
>> - Is there a way to access any kind of version control / or is the  
>> only access via downloading last stable version code?
>>  ( currently, read access would be enough )
>
>
> We have setup one: ImageJA at http://repo.or.cz/w/imageja.git/ ,  
> which is perhaps best used as a submodule of fiji  (web: http://pacific.mpi-cbg.de/ 
>    and repository: http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=summary 
>  )

So what would you recommend?, Fiji repository or ImageJA repository  
for developing ImageJ? I saw that Wayne merged his code into the  
ImageJA repo.
Are there any major differences between ImageJA and ImageJ (except the  
applet) on the desktop Version?
I think Fiji isn't the right place for us, because it is more designed  
for the end-user of imagej and not for the developer of it.
What is your opinion?
>
>
>> - Are there any manuels for NetBeans? I just found an older one http://www.mbl.edu/research/labs/adlc/CamAcqJ/NetBeansforIJDevelopment.html
>
>
> At the upcomming ImageJ conference, Volker Baecker will give an in-
> depth workshop on how to use Eclipse to develop for ImageJ.
> There are also some resources regarding IDE in the ImageJ  
> Documentation Wiki: http://imagejdocu.tudor.lu

I just found something for Eclipse, but this IDE doesn't work very  
well on a Mac Intel64 and so I am working with NetBeans.
Today I tried to fit the ImageJ Source into the NetBeans Folder  
structure. And it didn't work quite well, due to the build.xml file.
Maybe later this week :) I don't have any experience with ant yet.
Currently I just copied everything from the ImageJ Source to the src  
Folder in NetBeans. With the standart build.xml I can compile the  
ImageJ source.
The build.xml file is written with Netbeans, does nobody us it anymore?

>
>
>> - How can I supply patches? To whom?
>
>
> In Fiji, just use the contrib user which needs no password and  
> pushes only to the contrib branch.
> In ImageJA, use the mob user (same status as the contrib user in  
> Fiji).
>
> Some help here:
> http://pacific.mpi-cbg.de/wiki/index.php/Git_mini_howto
> http://pacific.mpi-cbg.de/wiki/index.php/Git
>
> On the other hand, Wayne preffers fully functional ij.jar, compiled  
> for java 1.4.2, along with the modified java files in full.
>
>
>
>>
>> Thanks and I appricate your help.
>
>
> You are welcome.
>
> Albert

- Thanks a lot -

Christian

[dscho]

Hi,

On Tue, 19 Aug 2008, Christian Lutz wrote:

> Am 19.08.2008 um 11:51 schrieb Albert Cardona:
>
> > Christian wrote:
> >
> > >- Is there a way to access any kind of version control / or is the
> > >  only access via downloading last stable version code?
> > > ( currently, read access would be enough )
> >
> >
> >We have setup one: ImageJA at http://repo.or.cz/w/imageja.git/ , which
> >is perhaps best used as a submodule of fiji (web:
> >http://pacific.mpi-cbg.de/ and repository:
> >http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=summary )
>
> So what would you recommend?, Fiji repository or ImageJA repository for
> developing ImageJ? I saw that Wayne merged his code into the ImageJA repo.

That is not completely correct: Wayne releases complete sources for the
ImageJ versions, which are then committed to the "imagej" branch of
ImageJA.  Since Wayne does not use Git, he is the author of those commits,
but not the committer.

> Are there any major differences between ImageJA and ImageJ (except the
> applet) on the desktop Version?

Unfortunately, there are a few more differences there.  However, I will be
working actively on reducing the differences, as one of the major goals of
ImageJA is to feed patches to ImageJ.

> I think Fiji isn't the right place for us, because it is more designed
> for the end-user of imagej and not for the developer of it.

It is correct that at the moment, Fiji is easier for the user than for the
developer.  However, I will be working (hard!) on making it much, much
easier for the developer.

The idea is that you can add a new plugin in a matter of minutes.  That
you will be able to develop in your favourite IDE.  That you can easily
debug things.  And that you can bundle it in a software package with a
single command.

Ciao,
Dscho

[Albert Cardona]

Hi Christian,,

>>> - Is there a way to access any kind of version control / or is the
>>> only access via downloading last stable version code?
>>>  ( currently, read access would be enough )
>>
>>
>> We have setup one: ImageJA at http://repo.or.cz/w/imageja.git/ ,
>> which is perhaps best used as a submodule of fiji  (web:
>> http://pacific.mpi-cbg.de/   and repository:
>> http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=summary )
>
> So what would you recommend?, Fiji repository or ImageJA repository
> for developing ImageJ? I saw that Wayne merged his code into the
> ImageJA repo.
> Are there any major differences between ImageJA and ImageJ (except the
> applet) on the desktop Version?
> I think Fiji isn't the right place for us, because it is more designed
> for the end-user of imagej and not for the developer of it.
> What is your opinion?

ImageJA has its own git source code repository. Fiji has a separate one.
Then, inside Fiji, ImageJA's git repository is registered as a
submodule, like a dependency.

Tinkering with ImageJ's source code is easiest with ImageJA's git
repository: see for example the wiki page on topic branches:

http://pacific.mpi-cbg.de/wiki/index.php/Git_topic_branches

You'll realize ImageJA has a lot of topic branches: we experiment with
it all the time. See the full list of pushed branches at the bottom of
this page, where it says "heads":

http://repo.or.cz/w/imageja.git/

For example, the head named "fiji" is a derivative branch, always
synchronized with the master branch, which we use as the kernel for Fiji.
Using git you can easily diff both branches. The main differences are at
the Menus.java class, which we have flexibilized. Now we can insert
plugin menu items anywhere in the menus from a plugins.config file.
There are ZERO fundamental differences between ImageJ and ImageJA on the
desktop.

As for general development: I do not use Eclipse, neither NetBeans. I
use shell+screen+ViM. For those that use Eclipse, though, there are git
plugins for it. I don't know about the state of NetBeans in relation to git.

Fiji has been created to make ImageJ + plugins trivial for end users
(via self-contained packages, see
http://pacific.mpi-cbg.de/wiki/index.php/Downloads ), while having a
full source code repository (ImageJ + plugins) available within a
version control system, for best ease of development. So Fiji targets
both: users and developers.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[dscho]

Hi,

On Wed, 20 Aug 2008, Albert Cardona wrote:

> As for general development: I do not use Eclipse, neither NetBeans. I
> use shell+screen+ViM. For those that use Eclipse, though, there are git
> plugins for it. I don't know about the state of NetBeans in relation to
> git.

FWIW I use shell+screen+vi, too.  As for the Git support of Eclipse: it is
starting to get usable, actually.  There is no Git support for NetBeans
yet.

Ciao,
Dscho

[Christian Lutz]

Hello,

Thank you for you help. Now, I got some perspektive how everything  
fits together.
And I will work with it some time.

best wishes
Christian




Am 20.08.2008 um 11:49 schrieb Albert Cardona:

> Hi Christian,,
>
>
>
>>>> - Is there a way to access any kind of version control / or is  
>>>> the only access via downloading last stable version code?
>>>> ( currently, read access would be enough )
>>>
>>>
>>> We have setup one: ImageJA at http://repo.or.cz/w/imageja.git/ ,  
>>> which is perhaps best used as a submodule of fiji  (web: http://pacific.mpi-cbg.de/ 
>>>    and repository: http://pacific.mpi-cbg.de/cgi-bin/gitweb.cgi?p=fiji.git;a=summary 
>>>  )
>>
>> So what would you recommend?, Fiji repository or ImageJA repository  
>> for developing ImageJ? I saw that Wayne merged his code into the  
>> ImageJA repo.
>> Are there any major differences between ImageJA and ImageJ (except  
>> the applet) on the desktop Version?
>> I think Fiji isn't the right place for us, because it is more  
>> designed for the end-user of imagej and not for the developer of it.
>> What is your opinion?
>
>
>
>
> ImageJA has its own git source code repository. Fiji has a separate  
> one.
> Then, inside Fiji, ImageJA's git repository is registered as a  
> submodule, like a dependency.
>
> Tinkering with ImageJ's source code is easiest with ImageJA's git  
> repository: see for example the wiki page on topic branches:
>
> http://pacific.mpi-cbg.de/wiki/index.php/Git_topic_branches
>
> You'll realize ImageJA has a lot of topic branches: we experiment  
> with it all the time. See the full list of pushed branches at the  
> bottom of this page, where it says "heads":
>
> http://repo.or.cz/w/imageja.git/
>
> For example, the head named "fiji" is a derivative branch, always  
> synchronized with the master branch, which we use as the kernel for  
> Fiji.
> Using git you can easily diff both branches. The main differences  
> are at the Menus.java class, which we have flexibilized. Now we can  
> insert plugin menu items anywhere in the menus from a plugins.config  
> file.
> There are ZERO fundamental differences between ImageJ and ImageJA on  
> the desktop.
>
> As for general development: I do not use Eclipse, neither NetBeans.  
> I use shell+screen+ViM. For those that use Eclipse, though, there  
> are git plugins for it. I don't know about the state of NetBeans in  
> relation to git.
>
> Fiji has been created to make ImageJ + plugins trivial for end users  
> (via self-contained packages, see http://pacific.mpi-cbg.de/wiki/index.php/Downloads 
>  ), while having a full source code repository (ImageJ + plugins)  
> available within a version control system, for best ease of  
> development. So Fiji targets both: users and developers.
>
> Albert
>
> --
> Albert Cardona
> http://www.mcdb.ucla.edu/Research/Hartenstein/acardona