finding objects of the same colour
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finding objects of the same colour
 
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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. |
Re: finding objects of the same colour
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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 |
Re: finding objects of the same colour
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W dniu 2014-10-03 11:38, Michael
Schmid-3 [via ImageJ] pisze:
Hi Ludwiczaka,Thank you very much. I'll try all the options right away and let know about the effects. Kind regards, Agnieszka. |
Re: finding objects of the same colour
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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 |
Re: finding objects of the same colour
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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 > -- 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: (001) 617-324-3747 Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: finding objects of the same colour
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In reply to this post by Stoyan Pavlov
W dniu 2014-10-04 01:39, Stoyan Pavlov
[via ImageJ] pisze:
Hi Ludwickzaka,Thank you very much. Regards, Agnieszka. |
Re: finding objects of the same colour
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In reply to this post by Ignacio Arganda-Carreras
W dniu 2014-10-04 11:03, Ignacio
Arganda-Carreras [via ImageJ] pisze:
Hello Agnieszka,Thank you for advice. I hope that my images processing is possible. Cheers, Agnieszka. |
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