Re: AnalyzeSkeleton 2D 3D - number of skeletons

[Daniel James White]

Hi Ignacio,

is there a (256?) limit to the number of skeletons that can be analysed
in the analyse skeletons 2D 3D ?

Senthil has more than that per image in some cases...

cheers

Dan


On Jul 17, 2009, at 6:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Wed, 15 Jul 2009 22:35:17 -0700
> From:    David Webster <[hidden email]>
> Subject: Re: AnalyzeSkeleton, problem solved
>
> Ignacio,
>
> As it turns out, the problem was caused by closing the "Tagged  
> Skeleton"
> image before the Results table was displayed. There is quite a delay  
> between
> image and results display, which is also why I didn't think it was  
> being
> displayed.
>
> So, al problems solved.
>
> David

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[David Webster]

Dan,

The ImageJ documentation says 255 skeletons, and the Fiji documentations
doesn't say. When I ran Maringa's example on the old imageJ (i.e feb 2009)
version I got 1096 skeletons, but it took *FOREVER *(well nearly) to produce
the results table and the log table. When I ran the Fiji version, it was
much faster but only produced a single results table entry and no log table.
From past experience, I think a break down by skeleton is desirable. It
would probably also be useful to have a information that would allow one to
indentify a skeletons at the image level. Unfortunately, I am a novice Java
programmer so I can't help Ignacio by doing these things (at leat for now).

david

On Fri, Jul 17, 2009 at 12:02 AM, Daniel James White <[hidden email]>wrote:

> Hi Ignacio,
>
> is there a (256?) limit to the number of skeletons that can be analysed
> in the analyse skeletons 2D 3D ?
>
> Senthil has more than that per image in some cases...
>
> cheers
>
> Dan
>
>
> On Jul 17, 2009, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
> Date:    Wed, 15 Jul 2009 22:35:17 -0700
>> From:    David Webster <[hidden email]>
>> Subject: Re: AnalyzeSkeleton, problem solved
>>
>> Ignacio,
>>
>> As it turns out, the problem was caused by closing the "Tagged Skeleton"
>> image before the Results table was displayed. There is quite a delay
>> between
>> image and results display, which is also why I didn't think it was being
>> displayed.
>>
>> So, al problems solved.
>>
>> David
>>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> +49  (0)351 210 2627 (Work phone at MPI-CBG)
> +49  (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net       BioImageXD
> http://pacific.mpi-cbg.de               Fiji is just ImageJ - Batteries
> Included
> http://www.chalkie.org.uk
> [hidden email]
> ( [hidden email] )
>

[Ignacio Arganda-Carreras]

David,

You are right, i just updated the wiki site with the new value (215-1
skeletons).

I have a debugging version of the code that displays every different
skeleton in a different color. If you need something like that, please, just
let me know.

Thanks for the feedback!

ignacio

On Fri, Jul 17, 2009 at 1:12 PM, David Webster <[hidden email]>wrote:

> Dan,
>
> The ImageJ documentation says 255 skeletons, and the Fiji documentations
> doesn't say. When I ran Maringa's example on the old imageJ (i.e feb 2009)
> version I got 1096 skeletons, but it took *FOREVER *(well nearly) to
> produce
> the results table and the log table. When I ran the Fiji version, it was
> much faster but only produced a single results table entry and no log
> table.
> From past experience, I think a break down by skeleton is desirable. It
> would probably also be useful to have a information that would allow one to
> indentify a skeletons at the image level. Unfortunately, I am a novice Java
> programmer so I can't help Ignacio by doing these things (at leat for now).
>
> david
>
> On Fri, Jul 17, 2009 at 12:02 AM, Daniel James White <[hidden email]
> >wrote:
>
> > Hi Ignacio,
> >
> > is there a (256?) limit to the number of skeletons that can be analysed
> > in the analyse skeletons 2D 3D ?
> >
> > Senthil has more than that per image in some cases...
> >
> > cheers
> >
> > Dan
> >
> >
> > On Jul 17, 2009, at 6:00 AM, IMAGEJ automatic digest system wrote:
> >
> > Date:    Wed, 15 Jul 2009 22:35:17 -0700
> >> From:    David Webster <[hidden email]>
> >> Subject: Re: AnalyzeSkeleton, problem solved
> >>
> >> Ignacio,
> >>
> >> As it turns out, the problem was caused by closing the "Tagged Skeleton"
> >> image before the Results table was displayed. There is quite a delay
> >> between
> >> image and results display, which is also why I didn't think it was being
> >> displayed.
> >>
> >> So, al problems solved.
> >>
> >> David
> >>
> >
> > Dr. Daniel James White BSc. (Hons.) PhD
> > Senior Microscopist / Image Visualisation, Processing and Analysis
> > Light Microscopy and Image Processing Facilities
> > Max Planck Institute of Molecular Cell Biology and Genetics
> > Pfotenhauerstrasse 108
> > 01307 DRESDEN
> > Germany
> >
> > [phone] (German Mobile)
> > +49  (0)351 210 2627 (Work phone at MPI-CBG)
> > +49  (0)351 210 1078 (Fax MPI-CBG LMF)
> >
> > http://www.bioimagexd.net       BioImageXD
> > http://pacific.mpi-cbg.de               Fiji is just ImageJ - Batteries
> > Included
> > http://www.chalkie.org.uk
> > [hidden email]
> > ( [hidden email] )
> >
>

--
Ignacio Arganda-Carreras, Ph.D.
Institute of Neuroinformatics
Uni/ETH Zurich
Winterthurerstrasse 190
Bau 55
Zurich 8057
[phone]

Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html

[David Webster]

Ignacio,

The floodgates are now open. Here are some suggestions I thought of.

1. Hmm! I think it would be useful to have  a "Skeleton Label" image where
each skeleton's pixels had a value equal to the skeleton's index number in
the results table. Is this what you get with your "colored" skeleton's.

2. Generally, a results table like that for the imageJ version that gives a
properties breakdown for each skeleton is better than the Fiji version.

3. If the initial and final point coordinates frm the log table could be
apppended to the rows in the results table, it would also be useful.

4. You might want to make the method visitSkeleton() public so it can be
used by other classes to re-traverse a skeleton. Does this make sense
Java-wise?

5. Make sure that the ImageJ and Fiji versions are the same.


On Fri, Jul 17, 2009 at 10:21 AM, Ignacio Arganda <[hidden email]
> wrote:

> David,
>
> You are right, i just updated the wiki site with the new value (215-1
> skeletons).
>
> I have a debugging version of the code that displays every different
> skeleton in a different color. If you need something like that, please,
> just
> let me know.
>
> Thanks for the feedback!
>
> ignacio
>
> On Fri, Jul 17, 2009 at 1:12 PM, David Webster <[hidden email]
> >wrote:
>
> > Dan,
> >
> > The ImageJ documentation says 255 skeletons, and the Fiji documentations
> > doesn't say. When I ran Maringa's example on the old imageJ (i.e feb
> 2009)
> > version I got 1096 skeletons, but it took *FOREVER *(well nearly) to
> > produce
> > the results table and the log table. When I ran the Fiji version, it was
> > much faster but only produced a single results table entry and no log
> > table.
> > From past experience, I think a break down by skeleton is desirable. It
> > would probably also be useful to have a information that would allow one
> to
> > indentify a skeletons at the image level. Unfortunately, I am a novice
> Java
> > programmer so I can't help Ignacio by doing these things (at leat for
> now).
> >
> > david
> >
> > On Fri, Jul 17, 2009 at 12:02 AM, Daniel James White <[hidden email]
> > >wrote:
> >
> > > Hi Ignacio,
> > >
> > > is there a (256?) limit to the number of skeletons that can be analysed
> > > in the analyse skeletons 2D 3D ?
> > >
> > > Senthil has more than that per image in some cases...
> > >
> > > cheers
> > >
> > > Dan
> > >
> > >
> > > On Jul 17, 2009, at 6:00 AM, IMAGEJ automatic digest system wrote:
> > >
> > > Date:    Wed, 15 Jul 2009 22:35:17 -0700
> > >> From:    David Webster <[hidden email]>
> > >> Subject: Re: AnalyzeSkeleton, problem solved
> > >>
> > >> Ignacio,
> > >>
> > >> As it turns out, the problem was caused by closing the "Tagged
> Skeleton"
> > >> image before the Results table was displayed. There is quite a delay
> > >> between
> > >> image and results display, which is also why I didn't think it was
> being
> > >> displayed.
> > >>
> > >> So, al problems solved.
> > >>
> > >> David
> > >>
> > >
> > > Dr. Daniel James White BSc. (Hons.) PhD
> > > Senior Microscopist / Image Visualisation, Processing and Analysis
> > > Light Microscopy and Image Processing Facilities
> > > Max Planck Institute of Molecular Cell Biology and Genetics
> > > Pfotenhauerstrasse 108
> > > 01307 DRESDEN
> > > Germany
> > >
> > > [phone] (German Mobile)
> > > +49  (0)351 210 2627 (Work phone at MPI-CBG)
> > > +49  (0)351 210 1078 (Fax MPI-CBG LMF)
> > >
> > > http://www.bioimagexd.net       BioImageXD
> > > http://pacific.mpi-cbg.de               Fiji is just ImageJ -
> Batteries
> > > Included
> > > http://www.chalkie.org.uk
> > > [hidden email]
> > > ( [hidden email] )
> > >
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institute of Neuroinformatics
> Uni/ETH Zurich
> Winterthurerstrasse 190
> Bau 55
> Zurich 8057
> [phone]
>
> Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html
>