imagej plugin
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Does anyone know if there is a plugin for ImageJ that will threshold an
image by color? If not, how does one segment a color image to identify particular structures, in this case nuclei? Thanks, carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 |
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There are many Color plugins for analyzing different types of color images. And once you have converted color into the values of a specific channel you should be able to threshold it the regular way.
Mike -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell Sent: Tuesday, April 14, 2009 1:43 PM To: [hidden email] Subject: imagej plugin Does anyone know if there is a plugin for ImageJ that will threshold an image by color? If not, how does one segment a color image to identify particular structures, in this case nuclei? Thanks, carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 |
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In reply to this post by Boswell, Carl A - (cboswell)
Hi Carl,
For the example image "HeLa Cells (1.3M, 48-bit RGB)" that comes with imageJ, the maxEntropy threshold of the MultiThresholder works best for nuclei. //run("HeLa Cells (1.3M, 48-bit RGB)"); run("Split Channels"); run("MultiThresholder", "Maximum Entropy apply"); Cheers, jens -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell Sent: Tuesday, April 14, 2009 19:43 PM To: [hidden email] Subject: imagej plugin Does anyone know if there is a plugin for ImageJ that will threshold an image by color? If not, how does one segment a color image to identify particular structures, in this case nuclei? Thanks, carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 |
 
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Boswell, Carl A - (cboswell) |
Re: imagej plugin
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In reply to this post by Boswell, Carl A - (cboswell)
HI All,
It's clear that I should have been more obvious about "color" in my query. I'm working with H&E stained slides, so color is really color, not pseudocolor, and there are subtleties to the shading and density of the colors. Sorry for the confusion. carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 ----- Original Message ----- From: "Joel Sheffield" <[hidden email]> To: "Carl Boswell" <[hidden email]> Sent: Tuesday, April 14, 2009 12:45 PM Subject: Re: imagej plugin > Assuming that you have labeled your nuclei with either DAPI or > Propidium Iodide, you can convert the color image into its three > components and threshold the one that isolates the nuclei. For DAPI, > depending on your filter set, the nuclei will appear in the blue > channel. We have a broad band emission filter on our UV cube, so we > also pick up a nice signal in the green channel. > > In a sense, you are using the color system of the camera to do a > color separation for you (assuming, of course, that you work in > primary colors). > >> Does anyone know if there is a plugin for ImageJ that will threshold an >> image by color? If not, how does one segment a color image to identify >> particular structures, in this case nuclei? >> Thanks, >> carl >> >> Carl A. Boswell, Ph.D. >> Molecular and Cellular Biology >> University of Arizona >> 520-954-7053 >> FAX 520-621-3709 > > > -- > Joel B. Sheffield, Ph.D. > Biology Department, Temple University > 1900 North 12th Street > Philadelphia, PA 19122 > [hidden email] > (215) 204 8839, fax (215) 204 0486 > http://astro.temple.edu/~jbs > > |
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Hi Carl,
I am not totally familiar with ImageJ but i do know that what you are asking can be done in MetaMorph. With MetaMorph you can manually set a range of RGB, HSL or HSI values to threshold your colour image. Alternatively you can click on the parts of the image you want thresholded and MetaMorph will build up the range based on the examples you give it. In the past i have had great success thresholding brown BAD, red AEC etc. I have not tried it on H and E but i can't see why it wouldn't work. So the question is i guess is there a plugin for ImageJ that can do the same function? I should note that i have no commercial tie to MetaMorph (or Molecular Devices) but have been a satisfied user for the last 4 years. Cheers Cam Cameron J. Nowell Microscopy Manager Centre for Advanced Microscopy Ludwig Institute for Cancer Research PO Box 2008 Royal Melbourne Hospital Victoria, 3050 AUSTRALIA Office: +61 3 9341 3155 Mobile: +61422882700 Fax: +61 3 9341 3104 Facility Website -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell Sent: Wednesday, 15 April 2009 7:49 AM To: [hidden email] Subject: Re: imagej plugin HI All, It's clear that I should have been more obvious about "color" in my query. I'm working with H&E stained slides, so color is really color, not pseudocolor, and there are subtleties to the shading and density of the colors. Sorry for the confusion. carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 ----- Original Message ----- From: "Joel Sheffield" <[hidden email]> To: "Carl Boswell" <[hidden email]> Sent: Tuesday, April 14, 2009 12:45 PM Subject: Re: imagej plugin > Assuming that you have labeled your nuclei with either DAPI or > Propidium Iodide, you can convert the color image into its three > components and threshold the one that isolates the nuclei. For DAPI, > depending on your filter set, the nuclei will appear in the blue > channel. We have a broad band emission filter on our UV cube, so we > also pick up a nice signal in the green channel. > > In a sense, you are using the color system of the camera to do a > color separation for you (assuming, of course, that you work in > primary colors). > >> Does anyone know if there is a plugin for ImageJ that will threshold >> image by color? If not, how does one segment a color image to identify >> particular structures, in this case nuclei? >> Thanks, >> carl >> >> Carl A. Boswell, Ph.D. >> Molecular and Cellular Biology >> University of Arizona >> 520-954-7053 >> FAX 520-621-3709 > > > -- > Joel B. Sheffield, Ph.D. > Biology Department, Temple University > 1900 North 12th Street > Philadelphia, PA 19122 > [hidden email] > (215) 204 8839, fax (215) 204 0486 > http://astro.temple.edu/~jbs > > No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.287 / Virus Database: 270.11.55/2057 - Release Date: 04/13/09 17:56:00 This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waiver any rights if you have received this communication in error. The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd. |
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In reply to this post by Boswell, Carl A - (cboswell)
There is actually a color measurement plugin available for ImageJ,
specifically for things like H&E. I haven't used it, though, so I can't vouch for its effectiveness. Here's the reference: http://www.dentistry.bham.ac.uk/landinig/software/cdeconv/cdeconv.html > HI All, > > It's clear that I should have been more obvious about "color" in my query. > I'm working with H&E stained slides, so color is really color, not > pseudocolor, and there are subtleties to the shading and density of the > colors. > Sorry for the confusion. > carl > > Carl A. Boswell, Ph.D. > Molecular and Cellular Biology > University of Arizona > 520-954-7053 > FAX 520-621-3709 > ----- Original Message ----- > From: "Joel Sheffield" <[hidden email]> > To: "Carl Boswell" <[hidden email]> > Sent: Tuesday, April 14, 2009 12:45 PM > Subject: Re: imagej plugin > > > > Assuming that you have labeled your nuclei with either DAPI or > > Propidium Iodide, you can convert the color image into its three > > components and threshold the one that isolates the nuclei. For DAPI, > > depending on your filter set, the nuclei will appear in the blue > > channel. We have a broad band emission filter on our UV cube, so we > > also pick up a nice signal in the green channel. > > > > In a sense, you are using the color system of the camera to do a > > color separation for you (assuming, of course, that you work in > > primary colors). > > > >> Does anyone know if there is a plugin for ImageJ that will threshold an > >> image by color? If not, how does one segment a color image to identify > >> particular structures, in this case nuclei? > >> Thanks, > >> carl > >> > >> Carl A. Boswell, Ph.D. > >> Molecular and Cellular Biology > >> University of Arizona > >> 520-954-7053 > >> FAX 520-621-3709 > > > > > > -- > > Joel B. Sheffield, Ph.D. > > Biology Department, Temple University > > 1900 North 12th Street > > Philadelphia, PA 19122 > > [hidden email] > > (215) 204 8839, fax (215) 204 0486 > > http://astro.temple.edu/~jbs > > > > -- Joel B. Sheffield, Ph.D. Biology Department, Temple University 1900 North 12th Street Philadelphia, PA 19122 [hidden email] (215) 204 8839, fax (215) 204 0486 http://astro.temple.edu/~jbs |
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In reply to this post by Boswell, Carl A - (cboswell)
Hi Carl,
I recommend the Colour Deconvolution plugin (http://www.dentistry.bham.ac.uk/landinig/software/cdeconv/cdeconv.html) or Threshold Colour, developed by Gabriel Landini (http://www.dentistry.bham.ac.uk/landinig/software/software.html ). The Colour Deconvolution plugin has some built-in tools for separating stains like H & E or Haematoxylin-DAB, etc. and it works very well for these standard stains. There is some good documentation available through the ImageJ website. I also have some notes on the plugins, which I can send you if you need further help. Cheers, Jacqui Jacqueline Ross Biomedical Imaging Microscopist Biomedical Imaging Research Unit School of Medical Sciences Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell Sent: Wednesday, 15 April 2009 9:49 a.m. To: [hidden email] Subject: Re: imagej plugin HI All, It's clear that I should have been more obvious about "color" in my query. I'm working with H&E stained slides, so color is really color, not pseudocolor, and there are subtleties to the shading and density of the colors. Sorry for the confusion. carl Carl A. Boswell, Ph.D. Molecular and Cellular Biology University of Arizona 520-954-7053 FAX 520-621-3709 ----- Original Message ----- From: "Joel Sheffield" <[hidden email]> To: "Carl Boswell" <[hidden email]> Sent: Tuesday, April 14, 2009 12:45 PM Subject: Re: imagej plugin > Assuming that you have labeled your nuclei with either DAPI or > Propidium Iodide, you can convert the color image into its three > components and threshold the one that isolates the nuclei. For DAPI, > depending on your filter set, the nuclei will appear in the blue > channel. We have a broad band emission filter on our UV cube, so we > also pick up a nice signal in the green channel. > > In a sense, you are using the color system of the camera to do a > color separation for you (assuming, of course, that you work in > primary colors). > >> Does anyone know if there is a plugin for ImageJ that will threshold >> image by color? If not, how does one segment a color image to identify >> particular structures, in this case nuclei? >> Thanks, >> carl >> >> Carl A. Boswell, Ph.D. >> Molecular and Cellular Biology >> University of Arizona >> 520-954-7053 >> FAX 520-621-3709 > > > -- > Joel B. Sheffield, Ph.D. > Biology Department, Temple University > 1900 North 12th Street > Philadelphia, PA 19122 > [hidden email] > (215) 204 8839, fax (215) 204 0486 > http://astro.temple.edu/~jbs > > |
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In reply to this post by Boswell, Carl A - (cboswell)
Carl,
The plugin "Threshold Colour" allows you to select (threshold) a specific color range, either in RGB, HSB, or CIE Lab color space. There is also a plugin named "Color Deconvolution" that allows you to separate "Channels" of a true color image, for example separate H&E and DAB hues from each other. You then would use conventional thresholding on your favorite "channel". Finally, you could separate the RGB channels of your image, or sometimes the YCM channels, and see which of those best represents your favorite structure. Many people have had good success converting HDAB images into CYM color space, separating the channels, and thresholding one of those such as yellow to identify and count brown or purple stained cells. -- Julio Vazquez, Fred Hutchinson Cancer Research Center Seattle, WA 98109-1024 On Apr 14, 2009, at 10:43 AM, Carl Boswell wrote:
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