Scholl analysis - Fiji

[Valori, Chiara /DZNE]

Dear everyone,

I'm performing Scholl analysis with the Fiji plugin "simple neurite tracer".  I have a question about the Sholl regression coefficient which is calculated in the results table: I do not understand what this number represents when cells are analyzed using standard axes. I get what it is when you use semi Log or Log-Log axes, but I thought you need a polynomial function for standard and thus more parameters...  could anyone please shed a bit of light in my confusion?

many thanks in advance,
Chiara





-------------------------------------------------------
Chiara Valori, PhD
German Centre for Neurodegenerative Diseases (DZNE) c/o TTR
Paul-Ehrlich-Str. 17
72076 Tübingen
Germany

phone: [phone] (office)
            [phone] (lab)
fax:     [phone]
email: [hidden email]
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Tiago Ferreira-2]

Hi Chiara,

On Sep 9, 2014, at 09:33, Valori, Chiara /DZNE <[hidden email]> wrote:
> I'm performing Scholl analysis with the Fiji plugin "simple neurite tracer".

Note that while Scholl is a common surname, it is irrelevant here.
The eponymous technique you are performing is named after Donald Sholl, the first
anatomist able to quantify the anatomy of neuronal arbors in single-cell labeling,
more than 60 years ago (See PMID 13117757 in http://fiji.sc/Sholl#References).


> I have a question about the Sholl regression coefficient which is calculated in
> the Results table: I do not understand what this number represents when cells are
> analyzed using standard axes.

In short: It means nothing when using linear axes, as it only applies to semi-log
or log-log transformations, as you suspected. So, why does SNT, reports it? I'm
guessing there were two reasons why Mark decided to report it at all times:

1) SNT features an extremely useful interactive prompt that automatically updates
   calculations every time a checkbox gets toggled. The calculations are performed
   in the background even when the user has chosen a combination of choices that
   do not make much sense. The plugin does not try to outsmart the user (wouldn't
   it be annoying otherwise?[1]) and just reports whatever calculations it was
   asked to.

2) Historically, ImageJ did not allow for non-mumeric text in the Results Table
   (this is no longer the case with recent versions of ImageJ). So including a
   non-numeric value for the Regression coefficient when using linear axes in the
   Results table, was not a feasible option.

That being said, we probably could change the plugin if you think this is a bug.
Note however that using log axes but choosing "No normalization" would not make
sense either. Hopefully this is all better explained throughout the
http://fiji.sc/Sholl documentation page (mainly http://fiji.sc/Sholl#MethodsTable).

> I thought you need a polynomial function for standard and thus more parameters...

You're also right. Linear axes (i.e, no normalizations to Area or Volume) would
require a polynomial fit. For that you would need to use Analyze>Sholl Analysis,
as indicated in http://fiji.sc/Sholl#Importing
This would also give you access to a wide repertoire of metrics, not available in
SNT.

Best,
-tiago

[1] In Sholl Analysis (Analyze>Sholl Analysis, http://fiji.sc/Sholl), the plugin
    does try to outsmart the user, and will automatically disable options that do
    not fulfill critical requirements. The consequence however, is that the prompt
    is not as streamlined as in SNT.
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Valori, Chiara /DZNE]

thanks so much for the comprehensive yet perfectly understandable reply

I do not think it's a bug, however I think it would be very helpful if you could copy paste the email you sent me within this tutorial
http://fiji.sc/Simple_Neurite_Tracer:_Sholl_analysis

thanks again,
Chiara


-------------------------------------------------------
Chiara Valori, PhD
German Centre for Neurodegenerative Diseases (DZNE) c/o TTR
Paul-Ehrlich-Str. 17
72076 Tübingen
Germany

phone: [phone] (office)
            [phone] (lab)
fax:     [phone]
email: [hidden email]
________________________________________
From: Tiago Ferreira [[hidden email]]
Sent: Tuesday, September 09, 2014 6:56 PM
To: [hidden email]
Cc: Valori, Chiara /DZNE
Subject: Re: Sholl analysis - Fiji (was Scholl analysis - Fiji)

Hi Chiara,

On Sep 9, 2014, at 09:33, Valori, Chiara /DZNE <[hidden email]> wrote:
> I'm performing Scholl analysis with the Fiji plugin "simple neurite tracer".

Note that while Scholl is a common surname, it is irrelevant here.
The eponymous technique you are performing is named after Donald Sholl, the first
anatomist able to quantify the anatomy of neuronal arbors in single-cell labeling,
more than 60 years ago (See PMID 13117757 in http://fiji.sc/Sholl#References).


> I have a question about the Sholl regression coefficient which is calculated in
> the Results table: I do not understand what this number represents when cells are
> analyzed using standard axes.

In short: It means nothing when using linear axes, as it only applies to semi-log
or log-log transformations, as you suspected. So, why does SNT, reports it? I'm
guessing there were two reasons why Mark decided to report it at all times:

1) SNT features an extremely useful interactive prompt that automatically updates
   calculations every time a checkbox gets toggled. The calculations are performed
   in the background even when the user has chosen a combination of choices that
   do not make much sense. The plugin does not try to outsmart the user (wouldn't
   it be annoying otherwise?[1]) and just reports whatever calculations it was
   asked to.

2) Historically, ImageJ did not allow for non-mumeric text in the Results Table
   (this is no longer the case with recent versions of ImageJ). So including a
   non-numeric value for the Regression coefficient when using linear axes in the
   Results table, was not a feasible option.

That being said, we probably could change the plugin if you think this is a bug.
Note however that using log axes but choosing "No normalization" would not make
sense either. Hopefully this is all better explained throughout the
http://fiji.sc/Sholl documentation page (mainly http://fiji.sc/Sholl#MethodsTable).

> I thought you need a polynomial function for standard and thus more parameters...

You're also right. Linear axes (i.e, no normalizations to Area or Volume) would
require a polynomial fit. For that you would need to use Analyze>Sholl Analysis,
as indicated in http://fiji.sc/Sholl#Importing
This would also give you access to a wide repertoire of metrics, not available in
SNT.

Best,
-tiago

[1] In Sholl Analysis (Analyze>Sholl Analysis, http://fiji.sc/Sholl), the plugin
    does try to outsmart the user, and will automatically disable options that do
    not fulfill critical requirements. The consequence however, is that the prompt
    is not as streamlined as in SNT.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Chiara,

> I think it would be very helpful if you could copy paste the email you
> sent me within this tutorial

You can edit the wiki yourself!

http://fiji.sc/Help:Contents#New_accounts
https://en.wikipedia.org/wiki/Wikipedia:Be_bold

Regards,
Curtis

On Tue, Sep 9, 2014 at 1:56 PM, Valori, Chiara /DZNE <[hidden email]>
wrote:

> thanks so much for the comprehensive yet perfectly understandable reply
>
> I do not think it's a bug, however I think it would be very helpful if you
> could copy paste the email you sent me within this tutorial
> http://fiji.sc/Simple_Neurite_Tracer:_Sholl_analysis
>
> thanks again,
> Chiara
>
>
> -------------------------------------------------------
> Chiara Valori, PhD
> German Centre for Neurodegenerative Diseases (DZNE) c/o TTR
> Paul-Ehrlich-Str. 17
> 72076 Tübingen
> Germany
>
> phone: [phone] (office)
>             [phone] (lab)
> fax:     [phone]
> email: [hidden email]
> ________________________________________
> From: Tiago Ferreira [[hidden email]]
> Sent: Tuesday, September 09, 2014 6:56 PM
> To: [hidden email]
> Cc: Valori, Chiara /DZNE
> Subject: Re: Sholl analysis - Fiji (was Scholl analysis - Fiji)
>
> Hi Chiara,
>
> On Sep 9, 2014, at 09:33, Valori, Chiara /DZNE <[hidden email]>
> wrote:
> > I'm performing Scholl analysis with the Fiji plugin "simple neurite
> tracer".
>
> Note that while Scholl is a common surname, it is irrelevant here.
> The eponymous technique you are performing is named after Donald Sholl,
> the first
> anatomist able to quantify the anatomy of neuronal arbors in single-cell
> labeling,
> more than 60 years ago (See PMID 13117757 in
> http://fiji.sc/Sholl#References).
>
>
> > I have a question about the Sholl regression coefficient which is
> calculated in
> > the Results table: I do not understand what this number represents when
> cells are
> > analyzed using standard axes.
>
> In short: It means nothing when using linear axes, as it only applies to
> semi-log
> or log-log transformations, as you suspected. So, why does SNT, reports
> it? I'm
> guessing there were two reasons why Mark decided to report it at all times:
>
> 1) SNT features an extremely useful interactive prompt that automatically
> updates
>    calculations every time a checkbox gets toggled. The calculations are
> performed
>    in the background even when the user has chosen a combination of
> choices that
>    do not make much sense. The plugin does not try to outsmart the user
> (wouldn't
>    it be annoying otherwise?[1]) and just reports whatever calculations it
> was
>    asked to.
>
> 2) Historically, ImageJ did not allow for non-mumeric text in the Results
> Table
>    (this is no longer the case with recent versions of ImageJ). So
> including a
>    non-numeric value for the Regression coefficient when using linear axes
> in the
>    Results table, was not a feasible option.
>
> That being said, we probably could change the plugin if you think this is
> a bug.
> Note however that using log axes but choosing "No normalization" would not
> make
> sense either. Hopefully this is all better explained throughout the
> http://fiji.sc/Sholl documentation page (mainly
> http://fiji.sc/Sholl#MethodsTable).
>
> > I thought you need a polynomial function for standard and thus more
> parameters...
>
> You're also right. Linear axes (i.e, no normalizations to Area or Volume)
> would
> require a polynomial fit. For that you would need to use Analyze>Sholl
> Analysis,
> as indicated in http://fiji.sc/Sholl#Importing
> This would also give you access to a wide repertoire of metrics, not
> available in
> SNT.
>
> Best,
> -tiago
>
> [1] In Sholl Analysis (Analyze>Sholl Analysis, http://fiji.sc/Sholl), the
> plugin
>     does try to outsmart the user, and will automatically disable options
> that do
>     not fulfill critical requirements. The consequence however, is that
> the prompt
>     is not as streamlined as in SNT.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html