OrientationJ

[Ndeye Birima Mbaye]

Hello,

I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.

I would like to trace the fibers obtained on the image. How to do ?


Thank you in advance.





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

[Herbie]

Good day,

you write:
"I have to characterize the fiber microstructure by finding their
orientations."
"When I use OrientationJ I get a curve that gives me the distribution of
angles."

Finding fiber orientations and getting their orientations appears related.

AFAIK, OrientationJ is not for tracing.
Fiber tracing is quite different from getting fiber orientations.

Please be more specific and post a typical image with detailed
explanations of what you like to determine.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:

> Hello,
>
> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>
> I would like to trace the fibers obtained on the image. How to do ?
>
>
> Thank you in advance.
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Ndeye Birima Mbaye]

In fact, I would like to find the preferential orientations and draw them on the image.

I attach you the image to study.



________________________________
De : ImageJ Interest Group <[hidden email]> de la part de Herbie <[hidden email]>
Envoyé : mardi 10 avril 2018 08:25
À : [hidden email]
Objet : Re: OrientationJ

Good day,

you write:
"I have to characterize the fiber microstructure by finding their
orientations."
"When I use OrientationJ I get a curve that gives me the distribution of
angles."

Finding fiber orientations and getting their orientations appears related.

AFAIK, OrientationJ is not for tracing.
Fiber tracing is quite different from getting fiber orientations.

Please be more specific and post a typical image with detailed
explanations of what you like to determine.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:

> Hello,
>
> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>
> I would like to trace the fibers obtained on the image. How to do ?
>
>
> Thank you in advance.
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ImageJ List<http://imagej.nih.gov/ij/list.html>

imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers. Subscribing To subscribe, go to the Subscribe or Unsubscribe page, enter your name and email address, and click "Subscribe (IMAGEJ)".


>

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

--
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[Herbie]

Good day,

attached please find the "Orientation Salience"-analysis that I've made
from the pre-processed sample image.
(Actually, the pre-processed image is DC-free, i.e. a 32bit bipolar image.)

The dominant orientation is at 133.5 degrees.
(Zero degree is horizontal and the angle increases counter-clockwise.)

Now please tell us exactly what you like to see as a result image.
Do you want to see the filtered image with only the dominant orientation?

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 11.04.18 um 10:48 schrieb Ndeye Birima Mbaye:

> In fact, I would like to find the preferential orientations and draw
> them on the image.
>
> I attach you the image to study.
>
>
>
>
> ------------------------------------------------------------------------
> *De :* ImageJ Interest Group <[hidden email]> de la part de Herbie
> <[hidden email]>
> *Envoyé :* mardi 10 avril 2018 08:25
> *À :* [hidden email]
> *Objet :* Re: OrientationJ
> Good day,
>
> you write:
> "I have to characterize the fiber microstructure by finding their
> orientations."
> "When I use OrientationJ I get a curve that gives me the distribution of
> angles."
>
> Finding fiber orientations and getting their orientations appears related.
>
> AFAIK, OrientationJ is not for tracing.
> Fiber tracing is quite different from getting fiber orientations.
>
> Please be more specific and post a typical image with detailed
> explanations of what you like to determine.
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:
>> Hello,
>>
>> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>>
>> I would like to trace the fibers obtained on the image. How to do ?
>>
>>
>> Thank you in advance.
>>
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> ImageJ List <http://imagej.nih.gov/ij/list.html>
> imagej.nih.gov
> home | news | docs | download | plugins | resources | list | links.
> ImageJ Mailing List The ImageJ mailing list is a discussion group for
> ImageJ users and developers. Subscribing To subscribe, go to the
> Subscribe or Unsubscribe page, enter your name and email address, and
> click "Subscribe (IMAGEJ)".
>
>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Ndeye Birima Mbaye]

Thank you very much. Yes that's exactly what I want to see and I would also like to know how you went about finding this result.

Regards,


________________________________
De : Herbie <[hidden email]>
Envoyé : mercredi 11 avril 2018 09:13
À : Ndeye Birima Mbaye; [hidden email]
Objet : Re: OrientationJ

Good day,

attached please find the "Orientation Salience"-analysis that I've made
from the pre-processed sample image.
(Actually, the pre-processed image is DC-free, i.e. a 32bit bipolar image.)

The dominant orientation is at 133.5 degrees.
(Zero degree is horizontal and the angle increases counter-clockwise.)

Now please tell us exactly what you like to see as a result image.
Do you want to see the filtered image with only the dominant orientation?

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 11.04.18 um 10:48 schrieb Ndeye Birima Mbaye:

> In fact, I would like to find the preferential orientations and draw
> them on the image.
>
> I attach you the image to study.
>
>
>
>
> ------------------------------------------------------------------------
> *De :* ImageJ Interest Group <[hidden email]> de la part de Herbie
> <[hidden email]>
> *Envoyé :* mardi 10 avril 2018 08:25
> *À :* [hidden email]
> *Objet :* Re: OrientationJ
> Good day,
>
> you write:
> "I have to characterize the fiber microstructure by finding their
> orientations."
> "When I use OrientationJ I get a curve that gives me the distribution of
> angles."
>
> Finding fiber orientations and getting their orientations appears related.
>
> AFAIK, OrientationJ is not for tracing.
> Fiber tracing is quite different from getting fiber orientations.
>
> Please be more specific and post a typical image with detailed
> explanations of what you like to determine.
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:
>> Hello,
>>
>> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>>
>> I would like to trace the fibers obtained on the image. How to do ?
>>
>>
>> Thank you in advance.
>>
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ImageJ List<http://imagej.nih.gov/ij/list.html>
imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers. Subscribing To subscribe, go to the Subscribe or Unsubscribe page, enter your name and email address, and click "Subscribe (IMAGEJ)".

> ImageJ List <http://imagej.nih.gov/ij/list.html>
> imagej.nih.gov
> home | news | docs | download | plugins | resources | list | links.
> ImageJ Mailing List The ImageJ mailing list is a discussion group for
> ImageJ users and developers. Subscribing To subscribe, go to the
> Subscribe or Unsubscribe page, enter your name and email address, and
> click "Subscribe (IMAGEJ)".
>
>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Herbie]

"Orientation Salience"-analyses are described in this report:
<gluender.de/Writings/WritingsTexts/WritingsDownloads/2013_Orientation.zip>

Please note that the report doesn't deal with the highpass filtering
that I've applied to your image in order to remove low frequency
fluctuations of your sample image.

As described in the report, "Orientation Salience" depends not only on
the geometric orientation of the pictorial structures but also on the
contrast of the structures!

If you need this analysis for a few images only, you may send them to me
offlist and I'll return the results.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 11.04.18 um 11:25 schrieb Ndeye Birima Mbaye:

> Thank you very much. Yes that's exactly what I want to see and I would
> also like to know how you went about finding this result.
>
> Regards,
>
>
>
> ------------------------------------------------------------------------
> *De :* Herbie <[hidden email]>
> *Envoyé :* mercredi 11 avril 2018 09:13
> *À :* Ndeye Birima Mbaye; [hidden email]
> *Objet :* Re: OrientationJ
> Good day,
>
> attached please find the "Orientation Salience"-analysis that I've made
> from the pre-processed sample image.
> (Actually, the pre-processed image is DC-free, i.e. a 32bit bipolar image.)
>
> The dominant orientation is at 133.5 degrees.
> (Zero degree is horizontal and the angle increases counter-clockwise.)
>
> Now please tell us exactly what you like to see as a result image.
> Do you want to see the filtered image with only the dominant orientation?
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 11.04.18 um 10:48 schrieb Ndeye Birima Mbaye:
>> In fact, I would like to find the preferential orientations and draw
>> them on the image.
>>
>> I attach you the image to study.
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>> *De :* ImageJ Interest Group <[hidden email]> de la part de Herbie
>> <[hidden email]>
>> *Envoyé :* mardi 10 avril 2018 08:25
>> *À :* [hidden email]
>> *Objet :* Re: OrientationJ
>> Good day,
>>
>> you write:
>> "I have to characterize the fiber microstructure by finding their
>> orientations."
>> "When I use OrientationJ I get a curve that gives me the distribution of
>> angles."
>>
>> Finding fiber orientations and getting their orientations appears related.
>>
>> AFAIK, OrientationJ is not for tracing.
>> Fiber tracing is quite different from getting fiber orientations.
>>
>> Please be more specific and post a typical image with detailed
>> explanations of what you like to determine.
>>
>> Regards
>>
>> Herbie
>>
>> ::::::::::::::::::::::::::::::::::::::::::::::::
>> Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:
>>> Hello,
>>>
>>> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>>>
>>> I would like to trace the fibers obtained on the image. How to do ?
>>>
>>>
>>> Thank you in advance.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> ImageJ List <http://imagej.nih.gov/ij/list.html>
> imagej.nih.gov
> home | news | docs | download | plugins | resources | list | links.
> ImageJ Mailing List The ImageJ mailing list is a discussion group for
> ImageJ users and developers. Subscribing To subscribe, go to the
> Subscribe or Unsubscribe page, enter your name and email address, and
> click "Subscribe (IMAGEJ)".
>
>
>> ImageJ List <http://imagej.nih.gov/ij/list.html>
>> imagej.nih.gov
>> home | news | docs | download | plugins | resources | list | links.
>> ImageJ Mailing List The ImageJ mailing list is a discussion group for
>> ImageJ users and developers. Subscribing To subscribe, go to the
>> Subscribe or Unsubscribe page, enter your name and email address, and
>> click "Subscribe (IMAGEJ)".
>>
>>
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Ndeye Birima Mbaye]

How did you do to have a more resolute image. What constant values did you apply to which variables?
I work on the quality of the image but I am not satisfied.


________________________________
De : Herbie <[hidden email]>
Envoyé : mercredi 11 avril 2018 09:38
À : Ndeye Birima Mbaye; [hidden email]
Objet : Re: OrientationJ

"Orientation Salience"-analyses are described in this report:
<gluender.de/Writings/WritingsTexts/WritingsDownloads/2013_Orientation.zip>

Please note that the report doesn't deal with the highpass filtering
that I've applied to your image in order to remove low frequency
fluctuations of your sample image.

As described in the report, "Orientation Salience" depends not only on
the geometric orientation of the pictorial structures but also on the
contrast of the structures!

If you need this analysis for a few images only, you may send them to me
offlist and I'll return the results.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::
Am 11.04.18 um 11:25 schrieb Ndeye Birima Mbaye:

> Thank you very much. Yes that's exactly what I want to see and I would
> also like to know how you went about finding this result.
>
> Regards,
>
>
>
> ------------------------------------------------------------------------
> *De :* Herbie <[hidden email]>
> *Envoyé :* mercredi 11 avril 2018 09:13
> *À :* Ndeye Birima Mbaye; [hidden email]
> *Objet :* Re: OrientationJ
> Good day,
>
> attached please find the "Orientation Salience"-analysis that I've made
> from the pre-processed sample image.
> (Actually, the pre-processed image is DC-free, i.e. a 32bit bipolar image.)
>
> The dominant orientation is at 133.5 degrees.
> (Zero degree is horizontal and the angle increases counter-clockwise.)
>
> Now please tell us exactly what you like to see as a result image.
> Do you want to see the filtered image with only the dominant orientation?
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 11.04.18 um 10:48 schrieb Ndeye Birima Mbaye:
>> In fact, I would like to find the preferential orientations and draw
>> them on the image.
>>
>> I attach you the image to study.
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>> *De :* ImageJ Interest Group <[hidden email]> de la part de Herbie
>> <[hidden email]>
>> *Envoyé :* mardi 10 avril 2018 08:25
>> *À :* [hidden email]
>> *Objet :* Re: OrientationJ
>> Good day,
>>
>> you write:
>> "I have to characterize the fiber microstructure by finding their
>> orientations."
>> "When I use OrientationJ I get a curve that gives me the distribution of
>> angles."
>>
>> Finding fiber orientations and getting their orientations appears related.
>>
>> AFAIK, OrientationJ is not for tracing.
>> Fiber tracing is quite different from getting fiber orientations.
>>
>> Please be more specific and post a typical image with detailed
>> explanations of what you like to determine.
>>
>> Regards
>>
>> Herbie
>>
>> ::::::::::::::::::::::::::::::::::::::::::::::::
>> Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:
>>> Hello,
>>>
>>> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>>>
>>> I would like to trace the fibers obtained on the image. How to do ?
>>>
>>>
>>> Thank you in advance.
>>>
>>>
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ImageJ List<http://imagej.nih.gov/ij/list.html>
imagej.nih.gov
home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers. Subscribing To subscribe, go to the Subscribe or Unsubscribe page, enter your name and email address, and click "Subscribe (IMAGEJ)".

> ImageJ List <http://imagej.nih.gov/ij/list.html>
> imagej.nih.gov
> home | news | docs | download | plugins | resources | list | links.
> ImageJ Mailing List The ImageJ mailing list is a discussion group for
> ImageJ users and developers. Subscribing To subscribe, go to the
> Subscribe or Unsubscribe page, enter your name and email address, and
> click "Subscribe (IMAGEJ)".
>
>
>> ImageJ List <http://imagej.nih.gov/ij/list.html>
>> imagej.nih.gov
>> home | news | docs | download | plugins | resources | list | links.
>> ImageJ Mailing List The ImageJ mailing list is a discussion group for
>> ImageJ users and developers. Subscribing To subscribe, go to the
>> Subscribe or Unsubscribe page, enter your name and email address, and
>> click "Subscribe (IMAGEJ)".
>>
>>
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Herbie]

Please study the report.

I don't use "OrientationJ".

Regards

Herbie


Am 11.04.18 um 11:43 schrieb Ndeye Birima Mbaye:

> How did you do to have a more resolute image. What constant values did you apply to which variables?
> I work on the quality of the image but I am not satisfied.
>
>
> ________________________________
> De : Herbie <[hidden email]>
> Envoyé : mercredi 11 avril 2018 09:38
> À : Ndeye Birima Mbaye; [hidden email]
> Objet : Re: OrientationJ
>
> "Orientation Salience"-analyses are described in this report:
> <gluender.de/Writings/WritingsTexts/WritingsDownloads/2013_Orientation.zip>
>
> Please note that the report doesn't deal with the highpass filtering
> that I've applied to your image in order to remove low frequency
> fluctuations of your sample image.
>
> As described in the report, "Orientation Salience" depends not only on
> the geometric orientation of the pictorial structures but also on the
> contrast of the structures!
>
> If you need this analysis for a few images only, you may send them to me
> offlist and I'll return the results.
>
> Regards
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::::::::
> Am 11.04.18 um 11:25 schrieb Ndeye Birima Mbaye:
>> Thank you very much. Yes that's exactly what I want to see and I would
>> also like to know how you went about finding this result.
>>
>> Regards,
>>
>>
>>
>> ------------------------------------------------------------------------
>> *De :* Herbie <[hidden email]>
>> *Envoyé :* mercredi 11 avril 2018 09:13
>> *À :* Ndeye Birima Mbaye; [hidden email]
>> *Objet :* Re: OrientationJ
>> Good day,
>>
>> attached please find the "Orientation Salience"-analysis that I've made
>> from the pre-processed sample image.
>> (Actually, the pre-processed image is DC-free, i.e. a 32bit bipolar image.)
>>
>> The dominant orientation is at 133.5 degrees.
>> (Zero degree is horizontal and the angle increases counter-clockwise.)
>>
>> Now please tell us exactly what you like to see as a result image.
>> Do you want to see the filtered image with only the dominant orientation?
>>
>> Regards
>>
>> Herbie
>>
>> ::::::::::::::::::::::::::::::::::::::::::::::::
>> Am 11.04.18 um 10:48 schrieb Ndeye Birima Mbaye:
>>> In fact, I would like to find the preferential orientations and draw
>>> them on the image.
>>>
>>> I attach you the image to study.
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *De :* ImageJ Interest Group <[hidden email]> de la part de Herbie
>>> <[hidden email]>
>>> *Envoyé :* mardi 10 avril 2018 08:25
>>> *À :* [hidden email]
>>> *Objet :* Re: OrientationJ
>>> Good day,
>>>
>>> you write:
>>> "I have to characterize the fiber microstructure by finding their
>>> orientations."
>>> "When I use OrientationJ I get a curve that gives me the distribution of
>>> angles."
>>>
>>> Finding fiber orientations and getting their orientations appears related.
>>>
>>> AFAIK, OrientationJ is not for tracing.
>>> Fiber tracing is quite different from getting fiber orientations.
>>>
>>> Please be more specific and post a typical image with detailed
>>> explanations of what you like to determine.
>>>
>>> Regards
>>>
>>> Herbie
>>>
>>> ::::::::::::::::::::::::::::::::::::::::::::::::
>>> Am 10.04.18 um 10:03 schrieb Ndeye Birima Mbaye:
>>>> Hello,
>>>>
>>>> I'm contacting you because I'm having trouble with the Imagej software. I have to characterize the fiber microstructure by finding their orientations. When I use OrientationJ I get a curve that gives me the distribution of angles.
>>>>
>>>> I would like to trace the fibers obtained on the image. How to do ?
>>>>
>>>>
>>>> Thank you in advance.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> ImageJ List<http://imagej.nih.gov/ij/list.html>
> imagej.nih.gov
> home | news | docs | download | plugins | resources | list | links. ImageJ Mailing List The ImageJ mailing list is a discussion group for ImageJ users and developers. Subscribing To subscribe, go to the Subscribe or Unsubscribe page, enter your name and email address, and click "Subscribe (IMAGEJ)".
>
>
>> ImageJ List <http://imagej.nih.gov/ij/list.html>
>> imagej.nih.gov
>> home | news | docs | download | plugins | resources | list | links.
>> ImageJ Mailing List The ImageJ mailing list is a discussion group for
>> ImageJ users and developers. Subscribing To subscribe, go to the
>> Subscribe or Unsubscribe page, enter your name and email address, and
>> click "Subscribe (IMAGEJ)".
>>
>>
>>> ImageJ List <http://imagej.nih.gov/ij/list.html>
>>> imagej.nih.gov
>>> home | news | docs | download | plugins | resources | list | links.
>>> ImageJ Mailing List The ImageJ mailing list is a discussion group for
>>> ImageJ users and developers. Subscribing To subscribe, go to the
>>> Subscribe or Unsubscribe page, enter your name and email address, and
>>> click "Subscribe (IMAGEJ)".
>>>
>>>
>>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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