Calculating porosity in a TIF image

[Seetha S]

Hi group,

I'm interested in quantifying the size of the pores (pores in a polymeric
membrane imaged by Confocal) in a TIF image. I have seen this being
previously done in literature and was wondering if a specific plug-in is
required for such an analysis.

Thank you in advance.

Regards,

--
Seetha S Manickam

[Michael Doube]

Seetha,

If your image is 2D, you can try the particle analyser under Analyze >
Analyze Particles.

If your image is 3D, you can try the particle analyser in BoneJ,
(http://bonej.org/particles) or the 3D object counter
http://rsbweb.nih.gov/ij/plugins/track/objects.html

and in Fiji (I think this is an updated version of the one at NIH)
http://pacific.mpi-cbg.de/wiki/index.php/3D_Object_Counter

Michael

On 09/08/10 21:44, Seetha S wrote:

> Hi group,
>
> I'm interested in quantifying the size of the pores (pores in a polymeric
> membrane imaged by Confocal) in a TIF image. I have seen this being
> previously done in literature and was wondering if a specific plug-in is
> required for such an analysis.
>
> Thank you in advance.
>
> Regards,
>

[Renaud Poincloux]

Hi group

It seems that there's a bug with the Stack/Orthogonal Views option if you
work with 16bit stacks.
Find enclosed orthogonal views of an LSM file 16bit (top left) that do not
take into account the correct voxel depth, and the correct orthogonal views
of the same file converted to RGB (bottom right).

Could someone correct this ?
Renaud Poincloux

[forodin]

Hi,
I'm currently working on a plugin for Fiji and I use Eclipse for it. I
dont use the FIJI source code or anything like that, I just copy / past
my code into the Plugins-New-Plugins - Window and run it from there. Not
that convenient.

What I would prefer is to run the code in Eclipse, have Fiji started and
the plugin executed automatically (and it would be even better if
everyone could do that from eclipse when using my code).

I can do that with ImageJ by adding a main-method to the plugin:

public static void main(String[] args) {
new ImageJ();
Optimized_Segmentation os = new Optimized_Segmentation();
os.run("");
}

(Optimized_Segmentation is my Plugin)

The thing is that it starts ImageJ, not FIJI. Can I do that with FIJI as
well?
I have to say I'm not very experienced neither in Java (had two lectures
on it) nor in ImageJ/Fiji (used it the first time 1 month ago).

Any comment on this would help. Thanks a lot in advance!

Jens
Osnabrück, Germany

[dscho]

Hi,

On Tue, 7 Sep 2010, Forodin wrote:

> I'm currently working on a plugin for Fiji and I use Eclipse for it. I
> dont use the FIJI source code or anything like that, I just copy / past
> my code into the Plugins-New-Plugins - Window and run it from there. Not
> that convenient.
>
> What I would prefer is to run the code in Eclipse, have Fiji started and
> the plugin executed automatically (and it would be even better if
> everyone could do that from eclipse when using my code).
>
> I can do that with ImageJ by adding a main-method to the plugin:
>
> public static void main(String[] args) {
> new ImageJ();
> Optimized_Segmentation os = new Optimized_Segmentation();
> os.run("");
> }

Try replacing ImageJ() with fiji.Main().

For those interested: fiji.Main() calls ImageJ(), but adds a little
infrastructure on top.

> (Optimized_Segmentation is my Plugin)

Would be nice to see/have your plugin...

Ciao,
Johannes

[Michael Doube]

Renaud,

It seems that this bug affects composite (multichannel) images, rather
than 16-bit images.  I can reproduce the bug using the Confocal Series
sample image, which is a 2-channel, 8-bit stack.

Michael

> It seems that there's a bug with the Stack/Orthogonal Views option if you
> work with 16bit stacks.
> Find enclosed orthogonal views of an LSM file 16bit (top left) that do not
> take into account the correct voxel depth, and the correct orthogonal views
> of the same file converted to RGB (bottom right).

[forodin]

Hey,
thx for your response! It didnt work, though, but I could set up eclipse
in a way that it exports all the needed files as a jar into fiji's
plugin directory. It's good enough.

I would publish the plugin but I had to sign a paper at my university
saying that I'm not allowed to until the final paper is out... it's
nothing spectacular, anyway :)

Greetings to all of you,
Jens