Simple Neurite Tracer plugin - analyze skeleton

[Rotem Oved]

  Hi all,
I'm trying to use the plugin called"simple neurite tracer" on fiji (under "segmentation"), tomeasure filaments length mostly. The plugin does seem to use the informationstored at the images in order to set a scale, and at the beginning, at thewindow called "all paths", it shows me the measurements in microns,just as I want them. However, when I go at the plugin's window to analysis-> analyze skeleton, the information that is given then does not match theprevious information, and we believe it is given in pixels (I attached an imageto demonstrate). Is there any way to convert that, so that all the informationwill appear in microns?
If something is unclear I would be morethan happy to explain what I meant.
Thank you very much. 

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[Ignacio Arganda-Carreras-2]

Hello Rotem,

That's indeed a bug. It should be fixed within the code but for now, what
you can do is to call Analayze Skeleton with the option to display the
skeletons, change the calibration of the skeletons manually (Image >
Properties) and then call the Analyze Skeleton plugin from the main menu.

I hope this helps!

ignacio

On Sun, Apr 12, 2015 at 11:04 AM, Rotem Oved <
[hidden email]> wrote:

>   Hi all,
> I'm trying to use the plugin called"simple neurite tracer" on fiji (under
> "segmentation"), tomeasure filaments length mostly. The plugin does seem to
> use the informationstored at the images in order to set a scale, and at the
> beginning, at thewindow called "all paths", it shows me the measurements in
> microns,just as I want them. However, when I go at the plugin's window to
> analysis-> analyze skeleton, the information that is given then does not
> match theprevious information, and we believe it is given in pixels (I
> attached an imageto demonstrate). Is there any way to convert that, so that
> all the informationwill appear in microns?
> If something is unclear I would be morethan happy to explain what I meant.
> Thank you very much.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

Tel : [phone] - fax : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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[Jan Eglinger]

Hi Ignacio and Rotem,

this bug can be fixed by keeping the calibration data of the original
image when creating the path image. I filed a pull request here:
https://github.com/fiji/Simple_Neurite_Tracer/pull/2

Jan


On 13.04.2015 10:26, Ignacio Arganda-Carreras wrote:

> Hello Rotem,
>
> That's indeed a bug. It should be fixed within the code but for now, what
> you can do is to call Analayze Skeleton with the option to display the
> skeletons, change the calibration of the skeletons manually (Image >
> Properties) and then call the Analyze Skeleton plugin from the main menu.
>
> I hope this helps!
>
> ignacio
>
> On Sun, Apr 12, 2015 at 11:04 AM, Rotem Oved <
> [hidden email]> wrote:
>
>>    Hi all,
>> I'm trying to use the plugin called"simple neurite tracer" on fiji (under
>> "segmentation"), tomeasure filaments length mostly. The plugin does seem to
>> use the informationstored at the images in order to set a scale, and at the
>> beginning, at thewindow called "all paths", it shows me the measurements in
>> microns,just as I want them. However, when I go at the plugin's window to
>> analysis-> analyze skeleton, the information that is given then does not
>> match theprevious information, and we believe it is given in pixels (I
>> attached an imageto demonstrate). Is there any way to convert that, so that
>> all the informationwill appear in microns?
>> If something is unclear I would be morethan happy to explain what I meant.
>> Thank you very much.
>>

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

[Ignacio Arganda-Carreras-2]

Thanks, Jan, you were faster than me ;)

On Mon, Apr 13, 2015 at 3:19 PM, Jan Eglinger <[hidden email]>
wrote:

> Hi Ignacio and Rotem,
>
> this bug can be fixed by keeping the calibration data of the original
> image when creating the path image. I filed a pull request here:
> https://github.com/fiji/Simple_Neurite_Tracer/pull/2
>
> Jan
>
>
>
> On 13.04.2015 10:26, Ignacio Arganda-Carreras wrote:
>
>> Hello Rotem,
>>
>> That's indeed a bug. It should be fixed within the code but for now, what
>> you can do is to call Analayze Skeleton with the option to display the
>> skeletons, change the calibration of the skeletons manually (Image >
>> Properties) and then call the Analyze Skeleton plugin from the main menu.
>>
>> I hope this helps!
>>
>> ignacio
>>
>> On Sun, Apr 12, 2015 at 11:04 AM, Rotem Oved <
>> [hidden email]> wrote:
>>
>>     Hi all,
>>> I'm trying to use the plugin called"simple neurite tracer" on fiji (under
>>> "segmentation"), tomeasure filaments length mostly. The plugin does seem
>>> to
>>> use the informationstored at the images in order to set a scale, and at
>>> the
>>> beginning, at thewindow called "all paths", it shows me the measurements
>>> in
>>> microns,just as I want them. However, when I go at the plugin's window to
>>> analysis-> analyze skeleton, the information that is given then does not
>>> match theprevious information, and we believe it is given in pixels (I
>>> attached an imageto demonstrate). Is there any way to convert that, so
>>> that
>>> all the informationwill appear in microns?
>>> If something is unclear I would be morethan happy to explain what I
>>> meant.
>>> Thank you very much.
>>>
>>>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

Tel : [phone] - fax : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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