Scholl Analysis

[ALEMBIC | Cesare]

Dear List,
does anyone perform  "Scholl analysis" to measure dendritic length and
the number of branch points in neurons ("intersection number") in ImageJ?

Thanks for any suggestions!

/Cesare


/
*/______________________________________________________________________________
/**/Dr. Cesare Covino
/*Biologist - Light Microscopy Coordinator*/
/**ALEMBIC*
Advanced Light and Electron Microscopy BioImaging Center  /
/DIBIT - /San Raffaele Scientific Institute//
/via Olgettina 58, 20132 - Milano - Italy /
/Tel [phone](others -4640, -4641)
Fax [phone]
e-mail: [hidden email]
ALEMBIC webpage: www.sanraffaele.org/research/alembic
<http://www.sanraffaele.org/58226.html>



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[Tiago Ferreira]

> Dear List,
> does anyone perform  "Scholl analysis" to measure dendritic length and
> the number of branch points in neurons ("intersection number") in ImageJ?
>
> Thanks for any suggestions!
>
> /Cesare

Cesare,

2D Sholl without reconstruction:
1) http://www-biology.ucsd.edu/labs/ghosh/software/
2) http://rsb.info.nih.gov/ij/plugins/concentric-circles.html
3) http://rsb.info.nih.gov/ij/macros/tools/ConcentricRingsTool.txt

2D Sholl with reconstruction
1) http://www.imagescience.org/meijering/software/neuronj/

3D Sholl:
1) http://www.personal.soton.ac.uk/dales/morpho/
2) http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/


Morphometric analysis:
http://krasnow.gmu.edu/L-Neuron/L-Neuron/LMeasure/index.htm

A good starting point is probably
Scorcioni et al. J. Comp. Neurol. (2004) vol. 473 (2) pp. 177-93
http://www.ncbi.nlm.nih.gov/pubmed/15101088,

Hope it helps,

T.

PS:
I think the original author was actually named Sholl, although by some
strange reason lots of people refer to it as School.
As far as I can tell this is the original reference:
Sholl DA (1953) Dendritic organization in the neurons of the visual and
motor cortices of the cat. J Anat 87: 387-406

[Anda Cornea]

Cesare,

I am using 3D Sholl by manually counting intersection of dendrites,
using the Cell  Counter plugin, with concentric spherical surfaces drawn
in ImageJ in confocal stacks.  The automatic Sholl analysis did not work
for me as in each field of view there are dendrites that do not belong
to the neuron investigated.  A comparison with 2D Sholl analysis done on
2D projections shows, as expected, more robust differences between
cases, particularly in the short radius range.  I am developing the
protocols right now so I am interested in any input that would make them
more useful.

Anda

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Cesare -ALEMBIC-
Sent: Tuesday, June 17, 2008 1:31 AM
To: [hidden email]
Subject: Scholl Analysis

Dear List,
does anyone perform  "Scholl analysis" to measure dendritic length and
the number of branch points in neurons ("intersection number") in
ImageJ?

Thanks for any suggestions!

/Cesare


/
*/______________________________________________________________________
________
/**/Dr. Cesare Covino
/*Biologist - Light Microscopy Coordinator*/
/**ALEMBIC*
Advanced Light and Electron Microscopy BioImaging Center  /
/DIBIT - /San Raffaele Scientific Institute//
/via Olgettina 58, 20132 - Milano - Italy /
/Tel [phone](others -4640, -4641)
Fax [phone]
e-mail: [hidden email]
ALEMBIC webpage: www.sanraffaele.org/research/alembic
<http://www.sanraffaele.org/58226.html>



********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Finanziamento agli enti della ricerca sanitaria")
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a [hidden email] o vai sul sito
www.5xmille.org

[Spiker]

I can not get UCSD program to work at all on my reconstructed image. Worse, I can not even get it to count a single line correctly in the picture. 

Tiago Ferreira wrote

> Dear List,
> does anyone perform  "Scholl analysis" to measure dendritic length and
> the number of branch points in neurons ("intersection number") in ImageJ?
>
> Thanks for any suggestions!
>
> /Cesare

Cesare,

2D Sholl without reconstruction:
1) http://www-biology.ucsd.edu/labs/ghosh/software/
2) http://rsb.info.nih.gov/ij/plugins/concentric-circles.html
3) http://rsb.info.nih.gov/ij/macros/tools/ConcentricRingsTool.txt

2D Sholl with reconstruction
1) http://www.imagescience.org/meijering/software/neuronj/

3D Sholl:
1) http://www.personal.soton.ac.uk/dales/morpho/
2) http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/


Morphometric analysis:
http://krasnow.gmu.edu/L-Neuron/L-Neuron/LMeasure/index.htm

A good starting point is probably
Scorcioni et al. J. Comp. Neurol. (2004) vol. 473 (2) pp. 177-93
http://www.ncbi.nlm.nih.gov/pubmed/15101088,

Hope it helps,

T.

PS:
I think the original author was actually named Sholl, although by some
strange reason lots of people refer to it as School.
As far as I can tell this is the original reference:
Sholl DA (1953) Dendritic organization in the neurons of the visual and
motor cortices of the cat. J Anat 87: 387-406