Tracing neurons in Sholl analysis

[Cris R]

Dear List,

I am trying to do Sholl analysis with the Sholl analysis plugin but I don't know which would be the best way of tracing the neurons. If you have any suggestion I would very much appreciate it.

Thank you,

Cris

[Mark Longair-2]

Cris R <[hidden email]> wrote:

>
> Dear List,
>
> I am trying to do Sholl analysis with the Sholl analysis plugin but I don't
> know which would be the best way of tracing the neurons. If you have any
> suggestion I would very much appreciate it.
>
> Thank you,
>
> Cris

Cris,

You could consider using Simple Neurite Tracer (bundled in Fiji)
for the tracing.  As it happens, I'm working at the moment on
adding Sholl analysis (a much requested feature!) [1] so
hopefully soon you'll be able to do everything with just that
plugin.

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

regards,
mark

  [1] http://longair.net/mark/sholl-work-in-progress.png

[Michael Ellis]

Can anyone explain what I'm doing wrong regarding using the ImageJ  
preferences?

After observing some strange behaviour I wrote this little
test plugin.

After setting a preference it then appears to fail to read it back.  
The IJ_Prefs.txt file gets written correctly though.

I've tried deleting the IJ_Prefs.txt file (incase there was some weird  
corruption). I'm running under OS-X with 10.5.8. I get the same result  
with ImageJ and ImageJ64.

I must be doing something really silly, but I just cannot see it!

---------------------------------------------------------------------------

import ij.*;
import ij.plugin.*;

public class My_Plugin implements PlugIn {

        public void run(String arg) {
                IJ.log("IJ.getVersion()=" + IJ.getVersion());
               
                final String prefName =  "wacky.myval";
                String prefValue = Prefs.getString(prefName, "Default Value");
               
                IJ.log(String.format("pref '%s' is '%s'\n", prefName, prefValue));
               
                prefValue = "New Value";
                IJ.log(String.format("Setting pref '%s' to '%s'", prefName,  
prefValue));
                Prefs.set(prefName, prefValue);
               
                Prefs.savePreferences();

                prefValue = Prefs.getString(prefName, "A default value that should  
not be seen!!!");
                IJ.log(String.format("pref '%s' is '%s'\n", prefName, prefValue));
        }
}

/*
--- Output -----------------------------
IJ.getVersion()=1.44c
pref 'wacky.myval' is 'Default Value'
Setting pref 'wacky.myval' to 'New Value'
pref 'wacky.myval' is 'A default value that should not be seen!!!'
------------------------------------------

After execution, the IJ_Prefs.txt file contains the line
.wacky.myval=NewValue
*/



Michael Ellis
Managing Director
Digital Scientific UK Ltd.
http://www.dsuk.co.uk
[hidden email]
tel: [phone]
fax: [phone]

Sheraton House
Castle Park
Cambridge
CB3 0AX


The contents of this e-mail may be privileged and are confidential.  
It may not be disclosed to or used by anyone other than the  
addressee(s), nor copied in any way.  If received in error, please  
advise the sender and delete it from your system.

[Michael Schmid]

Hi Michael,

there are two types of prefs commands, those adding KEY_PREFIX (a  
period) to the key, and those that don't and also search the Props  
inside the ij.jar. It seems that the latter are meant for ImageJ  
internal variables; getString is one of these.

Prefs.set(prefName, prefValue) adds a period, hence, your key is  
'.wacky.myval'

So it seems you should use Prefs.get instead of Prefs.getString:
   prefValue = Prefs.get(prefName, "A default value that should not  
be seen!!!");

Michael
________________________________________________________________

On 17 Jun 2010, at 15:11, [hidden email] wrote:

> Can anyone explain what I'm doing wrong regarding using the ImageJ  
> preferences?
>
> After observing some strange behaviour I wrote this little
> test plugin.
>
> After setting a preference it then appears to fail to read it back.  
> The IJ_Prefs.txt file gets written correctly though.
>
> I've tried deleting the IJ_Prefs.txt file (incase there was some  
> weird corruption). I'm running under OS-X with 10.5.8. I get the  
> same result with ImageJ and ImageJ64.
>
> I must be doing something really silly, but I just cannot see it!
>
> ----------------------------------------------------------------------
> -----
>
> import ij.*;
> import ij.plugin.*;
>
> public class My_Plugin implements PlugIn {
>
> public void run(String arg) {
> IJ.log("IJ.getVersion()=" + IJ.getVersion());
>
> final String prefName =  "wacky.myval";
> String prefValue = Prefs.getString(prefName, "Default Value");
>
> IJ.log(String.format("pref '%s' is '%s'\n", prefName, prefValue));
>
> prefValue = "New Value";
> IJ.log(String.format("Setting pref '%s' to '%s'", prefName,  
> prefValue));
> Prefs.set(prefName, prefValue);
>
> Prefs.savePreferences();
>
> prefValue = Prefs.getString(prefName, "A default value that  
> should not be seen!!!");
> IJ.log(String.format("pref '%s' is '%s'\n", prefName, prefValue));
> }
> }
>
> /*
> --- Output -----------------------------
> IJ.getVersion()=1.44c
> pref 'wacky.myval' is 'Default Value'
> Setting pref 'wacky.myval' to 'New Value'
> pref 'wacky.myval' is 'A default value that should not be seen!!!'
> ------------------------------------------
>
> After execution, the IJ_Prefs.txt file contains the line
> .wacky.myval=NewValue
> */
>
>
>
> Michael Ellis
> Managing Director
> Digital Scientific UK Ltd.
> http://www.dsuk.co.uk
> [hidden email]
> tel: [phone]
> fax: [phone]
>
> Sheraton House
> Castle Park
> Cambridge
> CB3 0AX
>
>
> The contents of this e-mail may be privileged and are  
> confidential.  It may not be disclosed to or used by anyone other  
> than the addressee(s), nor copied in any way.  If received in  
> error, please advise the sender and delete it from your system.

[dpoburko]

Dear Mark,

     I've just started using Simple Neurite Tracer, and it's awesome.
Strong Work! The tracing is great. But for some of my analysis, I need
to be able to calculate the minimum distance of some other marker to a
neuron. I previously used NeuonJ, which let me export all of the
vertices for each trace. I could then do the addition calculations in
Excel. So my question (/ feature request) is whether it's possible to
export the stored vertices that make up the traces/paths?

Many Thanks,
Damon


On 6/17/2010 1:26 AM, Mark Longair wrote:

> Cris R<[hidden email]>  wrote:
>    
>> Dear List,
>>
>> I am trying to do Sholl analysis with the Sholl analysis plugin but I don't
>> know which would be the best way of tracing the neurons. If you have any
>> suggestion I would very much appreciate it.
>>
>> Thank you,
>>
>> Cris
>>      
> Cris,
>
> You could consider using Simple Neurite Tracer (bundled in Fiji)
> for the tracing.  As it happens, I'm working at the moment on
> adding Sholl analysis (a much requested feature!) [1] so
> hopefully soon you'll be able to do everything with just that
> plugin.
>
>    http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer
>
> regards,
> mark
>
>    [1] http://longair.net/mark/sholl-work-in-progress.png
>    

[Mark Longair-2]

Damon Poburko <[hidden email]> wrote:

>
> Dear Mark,
>
>     I've just started using Simple Neurite Tracer, and it's
> awesome. Strong Work! The tracing is great. But for some of my
> analysis, I need to be able to calculate the minimum distance of some
> other marker to a neuron. I previously used NeuonJ, which let me
> export all of the vertices for each trace. I could then do the
> addition calculations in Excel. So my question (/ feature request) is
> whether it's possible to export the stored vertices that make up the
> traces/paths?
>
> Many Thanks,
> Damon

Damon,

Thanks for your kind remarks.  The .traces file that you save
from the plugin has information about all the vertices - it's
just gzipped XML, and the format is described here:

  http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/file-format.html

As you've probably seen, you can also export higher level
information about the files via the "Export as CSV" option, but
that doesn't have vertex level information - only the .traces
file does at the moment.

As ever, I'm very open to patches to provide other features that
people might need.

regards,
mark

[Mark Longair-2]

Cris,

There is now an interface for doing Sholl analysis in the
current version of Simple Neurite Tracer.  (You should do
"Help > Update Fiji" to make that you have the newest version.)

I would still regard this feature as experimental, since it's
new and the results haven't been validated against any other
data.  There is a tutorial here:

  http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer%3A_Sholl_analysis

I would be interested in any feedback, or suggestions for
pre-analyzed data that could be used for validation.

regards,
mark

[.. no next text below ..]

Mark Longair <[hidden email]> wrote:

>
> Cris R <[hidden email]> wrote:
>>
>> Dear List,
>>
>> I am trying to do Sholl analysis with the Sholl analysis plugin but I don't
>> know which would be the best way of tracing the neurons. If you have any
>> suggestion I would very much appreciate it.
>>
>> Thank you,
>>
>> Cris
>
> Cris,
>
> You could consider using Simple Neurite Tracer (bundled in Fiji)
> for the tracing.  As it happens, I'm working at the moment on
> adding Sholl analysis (a much requested feature!) [1] so
> hopefully soon you'll be able to do everything with just that
> plugin.
>
>   http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer 
>
> regards,
> mark
>
>   [1] http://longair.net/mark/sholl-work-in-progress.png