finding objects of the same colour

[ludwiczakagnieszka]

Hi everyone.

I'm working on images of muscles anatomical and ultrasonic images. My aim is to detect marbling - its the fat inside the muscle, visible on the muscle cross section in form of a net of white particles. I've already tried tresholding and different edge detectors. Tresholding seems do be the best so far, but the edge detectors work unproperly on the type of images I'm working with. I want to find some additional tool except for the tresholding.  Maybe it should find objects with thi same colour?? Maybe you can give me some guidelines what may be the best for this purpose?

Thank you in advance.

[Michael Schmid]

Hi Ludwiczaka,

a few ideas:

- Try edge sharpening, e.g. use the 'Thresholded Blur' plugin, it can be also used to sharpen edges
  http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start

- If you have an RGB image with different colors, try Gabriel Landini's color deconvolution plugin (built-in in Fiji)
  http://www.mecourse.com/landinig/software/software.html
or the Versatile wand (in contrast to the Wand of ImageJ, it's color sensitive)
  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

Michael
________________________________________________________________

On Oct 3, 2014, at 09:13, ludwiczakagnieszka wrote:

> Hi everyone.
>
> I'm working on images of muscles anatomical and ultrasonic images. My aim is
> to detect marbling - its the fat inside the muscle, visible on the muscle
> cross section in form of a net of white particles. I've already tried
> tresholding and different edge detectors. Tresholding seems do be the best
> so far, but the edge detectors work unproperly on the type of images I'm
> working with. I want to find some additional tool except for the
> tresholding.  Maybe it should find objects with thi same colour?? Maybe you
> can give me some guidelines what may be the best for this purpose?
>
> Thank you in advance.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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

[ludwiczakagnieszka]

W dniu 2014-10-03 11:38, Michael Schmid-3 [via ImageJ] pisze:

Hi Ludwiczaka,

a few ideas:

- Try edge sharpening, e.g. use the 'Thresholded Blur' plugin, it can be also used to sharpen edges
  http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start

- If you have an RGB image with different colors, try Gabriel Landini's color deconvolution plugin (built-in in Fiji)
  http://www.mecourse.com/landinig/software/software.html
or the Versatile wand (in contrast to the Wand of ImageJ, it's color sensitive)
  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start

Michael
________________________________________________________________

On Oct 3, 2014, at 09:13, ludwiczakagnieszka wrote:

> Hi everyone.
>
> I'm working on images of muscles anatomical and ultrasonic images. My aim is
> to detect marbling - its the fat inside the muscle, visible on the muscle
> cross section in form of a net of white particles. I've already tried
> tresholding and different edge detectors. Tresholding seems do be the best
> so far, but the edge detectors work unproperly on the type of images I'm
> working with. I want to find some additional tool except for the
> tresholding.  Maybe it should find objects with thi same colour?? Maybe you
> can give me some guidelines what may be the best for this purpose?
>
> Thank you in advance.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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---

If you reply to this email, your message will be added to the discussion below:

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NAML

... [show rest of quote]

Thank you very much. I'll try all the options right away and let know about the effects.

Kind regards,
Agnieszka.

[Stoyan Pavlov]

Hi Ludwickzaka,
Seems like you need to combine several different approaches - color based,
shape and texture...  You may try the Weka segmentation (build into Fiji),
or Cell profiler (separate software based on ImageJ).

Best wishes
Stoyan
 На 03.10.2014 20:08 "ludwiczakagnieszka" <[hidden email]>
написа:

> W dniu 2014-10-03 11:38, Michael Schmid-3 [via ImageJ] pisze:
> > Hi Ludwiczaka,
> >
> > a few ideas:
> >
> > - Try edge sharpening, e.g. use the 'Thresholded Blur' plugin, it can
> > be also used to sharpen edges
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
> >
> > - If you have an RGB image with different colors, try Gabriel
> > Landini's color deconvolution plugin (built-in in Fiji)
> > http://www.mecourse.com/landinig/software/software.html
> > or the Versatile wand (in contrast to the Wand of ImageJ, it's color
> > sensitive)
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
> >
> > Michael
> > ________________________________________________________________
> >
> > On Oct 3, 2014, at 09:13, ludwiczakagnieszka wrote:
> >
> > > Hi everyone.
> > >
> > > I'm working on images of muscles anatomical and ultrasonic images.
> > My aim is
> > > to detect marbling - its the fat inside the muscle, visible on the
> > muscle
> > > cross section in form of a net of white particles. I've already tried
> > > tresholding and different edge detectors. Tresholding seems do be
> > the best
> > > so far, but the edge detectors work unproperly on the type of images
> > I'm
> > > working with. I want to find some additional tool except for the
> > > tresholding.  Maybe it should find objects with thi same colour??
> > Maybe you
> > > can give me some guidelines what may be the best for this purpose?
> > >
> > > Thank you in advance.
> > >
> > >
> > >
> > > --
> > > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883.html
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> >
> > ------------------------------------------------------------------------
> > If you reply to this email, your message will be added to the
> > discussion below:
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009886.html
> >
> > To unsubscribe from finding objects of the same colour, click here
> > <
> >.
> > NAML
> > <
> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
> >
> >
> Thank you very much. I'll try all the options right away and let know
> about the effects.
>
> Kind regards,
> Agnieszka.
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009896.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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

[Ignacio Arganda-Carreras]

Hello Agnieszka,

You might also be interested on using SIOX:

http://fiji.sc/SIOX

Cheers!

ignacio


On Sat, Oct 4, 2014 at 1:36 AM, Stoyan Pavlov <[hidden email]>
wrote:

> Hi Ludwickzaka,
> Seems like you need to combine several different approaches - color based,
> shape and texture...  You may try the Weka segmentation (build into Fiji),
> or Cell profiler (separate software based on ImageJ).
>
> Best wishes
> Stoyan
>  На 03.10.2014 20:08 "ludwiczakagnieszka" <[hidden email]>
> написа:
>
> > W dniu 2014-10-03 11:38, Michael Schmid-3 [via ImageJ] pisze:
> > > Hi Ludwiczaka,
> > >
> > > a few ideas:
> > >
> > > - Try edge sharpening, e.g. use the 'Thresholded Blur' plugin, it can
> > > be also used to sharpen edges
> > >
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
> > >
> > > - If you have an RGB image with different colors, try Gabriel
> > > Landini's color deconvolution plugin (built-in in Fiji)
> > > http://www.mecourse.com/landinig/software/software.html
> > > or the Versatile wand (in contrast to the Wand of ImageJ, it's color
> > > sensitive)
> > >
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
> > >
> > > Michael
> > > ________________________________________________________________
> > >
> > > On Oct 3, 2014, at 09:13, ludwiczakagnieszka wrote:
> > >
> > > > Hi everyone.
> > > >
> > > > I'm working on images of muscles anatomical and ultrasonic images.
> > > My aim is
> > > > to detect marbling - its the fat inside the muscle, visible on the
> > > muscle
> > > > cross section in form of a net of white particles. I've already tried
> > > > tresholding and different edge detectors. Tresholding seems do be
> > > the best
> > > > so far, but the edge detectors work unproperly on the type of images
> > > I'm
> > > > working with. I want to find some additional tool except for the
> > > > tresholding.  Maybe it should find objects with thi same colour??
> > > Maybe you
> > > > can give me some guidelines what may be the best for this purpose?
> > > >
> > > > Thank you in advance.
> > > >
> > > >
> > > >
> > > > --
> > > > View this message in context:
> > >
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883.html
> > > > Sent from the ImageJ mailing list archive at Nabble.com.
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > > If you reply to this email, your message will be added to the
> > > discussion below:
> > >
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009886.html
> > >
> > > To unsubscribe from finding objects of the same colour, click here
> > > <
> >
> > >.
> > > NAML
> > > <
> >
> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
> > >
> > >
> > Thank you very much. I'll try all the options right away and let know
> > about the effects.
> >
> > Kind regards,
> > Agnieszka.
> >
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009896.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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

[ludwiczakagnieszka]

W dniu 2014-10-04 01:39, Stoyan Pavlov [via ImageJ] pisze:

Hi Ludwickzaka,
Seems like you need to combine several different approaches - color based,
shape and texture...  You may try the Weka segmentation (build into Fiji),
or Cell profiler (separate software based on ImageJ).

Best wishes
Stoyan
 На 03.10.2014 20:08 "ludwiczakagnieszka" <[hidden email]>
написа:

> W dniu 2014-10-03 11:38, Michael Schmid-3 [via ImageJ] pisze:
> > Hi Ludwiczaka,
> >
> > a few ideas:
> >
> > - Try edge sharpening, e.g. use the 'Thresholded Blur' plugin, it can
> > be also used to sharpen edges
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
> >
> > - If you have an RGB image with different colors, try Gabriel
> > Landini's color deconvolution plugin (built-in in Fiji)
> > http://www.mecourse.com/landinig/software/software.html
> > or the Versatile wand (in contrast to the Wand of ImageJ, it's color
> > sensitive)
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
> >
> > Michael
> > ________________________________________________________________
> >
> > On Oct 3, 2014, at 09:13, ludwiczakagnieszka wrote:
> >
> > > Hi everyone.
> > >
> > > I'm working on images of muscles anatomical and ultrasonic images.
> > My aim is
> > > to detect marbling - its the fat inside the muscle, visible on the
> > muscle
> > > cross section in form of a net of white particles. I've already tried
> > > tresholding and different edge detectors. Tresholding seems do be
> > the best
> > > so far, but the edge detectors work unproperly on the type of images
> > I'm
> > > working with. I want to find some additional tool except for the
> > > tresholding.  Maybe it should find objects with thi same colour??
> > Maybe you
> > > can give me some guidelines what may be the best for this purpose?
> > >
> > > Thank you in advance.
> > >
> > >
> > >
> > > --
> > > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883.html
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> >
> > ------------------------------------------------------------------------
> > If you reply to this email, your message will be added to the
> > discussion below:
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009886.html
> >
> > To unsubscribe from finding objects of the same colour, click here
> > <
> >.
> > NAML
> > <
> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
> >
> >
> Thank you very much. I'll try all the options right away and let know
> about the effects.
>
> Kind regards,
> Agnieszka.
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009896.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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

---

If you reply to this email, your message will be added to the discussion below:

http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009899.html

To unsubscribe from finding objects of the same colour, click here.
NAML

... [show rest of quote]

Thank you very much.

Regards,
Agnieszka.

[ludwiczakagnieszka]

W dniu 2014-10-04 11:03, Ignacio Arganda-Carreras [via ImageJ] pisze:

Hello Agnieszka,

You might also be interested on using SIOX:

http://fiji.sc/SIOX

Cheers!

ignacio


On Sat, Oct 4, 2014 at 1:36 AM, Stoyan Pavlov <[hidden email]>
wrote:

> Hi Ludwickzaka,
> Seems like you need to combine several different approaches - color based,
> shape and texture...  You may try the Weka segmentation (build into Fiji),
> or Cell profiler (separate software based on ImageJ).
>
> Best wishes
> Stoyan
>  На 03.10.2014 20:08 "ludwiczakagnieszka" <[hidden email]>
> написа:
>
> > W dniu 2014-10-03 11:38, Michael Schmid-3 [via ImageJ] pisze:
> > > Hi Ludwiczaka,
> > >
> > > a few ideas:
> > >
> > > - Try edge sharpening, e.g. use the 'Thresholded Blur' plugin, it can
> > > be also used to sharpen edges
> > >
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
> > >
> > > - If you have an RGB image with different colors, try Gabriel
> > > Landini's color deconvolution plugin (built-in in Fiji)
> > > http://www.mecourse.com/landinig/software/software.html
> > > or the Versatile wand (in contrast to the Wand of ImageJ, it's color
> > > sensitive)
> > >
> >
> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
> > >
> > > Michael
> > > ________________________________________________________________
> > >
> > > On Oct 3, 2014, at 09:13, ludwiczakagnieszka wrote:
> > >
> > > > Hi everyone.
> > > >
> > > > I'm working on images of muscles anatomical and ultrasonic images.
> > > My aim is
> > > > to detect marbling - its the fat inside the muscle, visible on the
> > > muscle
> > > > cross section in form of a net of white particles. I've already tried
> > > > tresholding and different edge detectors. Tresholding seems do be
> > > the best
> > > > so far, but the edge detectors work unproperly on the type of images
> > > I'm
> > > > working with. I want to find some additional tool except for the
> > > > tresholding.  Maybe it should find objects with thi same colour??
> > > Maybe you
> > > > can give me some guidelines what may be the best for this purpose?
> > > >
> > > > Thank you in advance.
> > > >
> > > >
> > > >
> > > > --
> > > > View this message in context:
> > >
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883.html
> > > > Sent from the ImageJ mailing list archive at Nabble.com.
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > > If you reply to this email, your message will be added to the
> > > discussion below:
> > >
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009886.html
> > >
> > > To unsubscribe from finding objects of the same colour, click here
> > > <
> >
> > >.
> > > NAML
> > > <
> >
> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
> > >
> > >
> > Thank you very much. I'll try all the options right away and let know
> > about the effects.
> >
> > Kind regards,
> > Agnieszka.
> >
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009896.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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

---

If you reply to this email, your message will be added to the discussion below:

http://imagej.1557.x6.nabble.com/finding-objects-of-the-same-colour-tp5009883p5009901.html

To unsubscribe from finding objects of the same colour, click here.
NAML

... [show rest of quote]

Thank you for advice. I hope that my images processing is possible.

Cheers,
Agnieszka.