http://imagej.273.s1.nabble.com/Color-thresholding-and-obtaining-Lab-values-tp5020700p5020744.html
Dr. Straatman,
thresholding. Thank you very much for your help!
> To be fair the alternative is that you don't use the ROI Manager:
>
> 1. Open --> Open photo, which is an RGB color image.
> 2. Image --> Adjust --> Color threshold... --> Set the threshold of L*
> value to be 71-216 so that the black and white parts will be excluded. -->
> Select.
> 3. The yellow parts (of which I want to know the Lab values) are circled
> with yellow lines now.
> 4. Image --> Type --> Lab stack.
> 5. Edit --> Selection --> Restore selection (The outline of my ROI comes
> back on the Lab stack images)
> 6. Plugins --> Stack --> Measure stack
>
> Kees
>
>
> -----Original Message-----
> From: Straatman, Kees (Dr.) [mailto:
[hidden email]]
> Sent: 29 May 2018 09:13
> To:
[hidden email]
> Subject: Re: Color thresholding and obtaining Lab values
>
> Dear Rie,
>
> As your selection is already in the ROI Manager you don't need to restore
> the overlay
>
> 1. Open --> Open photo, which is an RGB color image.
> 2. Image --> Adjust --> Color threshold... --> Set the threshold of L*
> value to be 71-216 so that the black and white parts will be excluded. -->
> Select.
> 3. The yellow parts (of which I want to know the Lab values) are circled
> with yellow lines now.
> 4. Edit --> Selection --> Add to manager 5. Image --> Type --> Lab stack.
> 6. In the ROI Manager menu select More --> Multi Measure; in the menu
> presented, select "Measure all 3 slices" and deselect "One row per slice"
>
> Best wishes
>
> Kees
>
>
> -----Original Message-----
> From: Rie Sadohara [mailto:
[hidden email]]
> Sent: 26 May 2018 21:59
> To:
[hidden email]
> Subject: Re: Color thresholding and obtaining Lab values
>
> Hello Dr. Straatman,
>
> I cannot switch steps 4 and 5; I need to add the thresholded area to
> manager as in step 4 before converting the image into Lab stack because Lab
> stack conversion deletes currently selected area. If I convert the original
> image into Lab stack first then try to color-threshold, it does not work
> because the Threshold color window turns blank and I cannot do any
> color-thresholding. So, before converting the image into Lab stack, I need
> to do color-thresholding with the original image and save the thresholded
> area to manager so that I can use it on the Lab-converted image. Those
> steps are the only order that works, I think, because color thresholding
> can only be done on the RGB image, and L a b values can only be measured on
> a Lab stack image. Does it make sense?
>
> As for doing the measurements via the ROI manager (multimeasure), yes it
> gives the same results as step 7. Actually the first bullet point of step 4
> does the same thing as step 7. Below is the correct complete steps.
> Restoring the selection (step 6) is still necessary as selection will be
> lost when the image is converted to Lab stack.
>
> 1. Open --> Open my photo, which is an RGB color image.
> 2. Image --> Adjust --> Color threshold... --> Set the threshold of L*
> value to be 71-216 so that the black and white parts will be excluded. -->
> Select.
> 3. The yellow parts (of which I want to know the Lab values) are circled
> with yellow lines now.
> 4. Edit --> Selection --> Add to manager
> - in the menu presented, select "Measure all 3 slices" and deselect
> "One row per slice"
> 5. Image --> Type --> Lab stack.
> 6. Edit --> Selection --> Restore selection (The outline of my ROI comes
> back on the Lab stack images) 7. In the ROI Manager menus select More -->
> Multi Measure
> Or alternatively, Plugins --> Stack --> Measure stack
>
> Thank you very much!!
>
> Rie
>
>
>
> On 25 May 2018 at 12:30, Straatman, Kees (Dr.) <
[hidden email]>
> wrote:
>
> > Hi Rie,
> >
> > I think you have to switch steps 4 and 5, or at least do the
> > measurements via the ROI manager after step 5. I don't think you need
> > step 6 and 7 unless I miss what you plan to do.
> >
> > Best wishes
> >
> > Kees
> >
> > -----Original Message-----
> > From: Rie Sadohara [mailto:
[hidden email]]
> > Sent: 24 May 2018 18:16
> > To:
[hidden email]
> > Subject: Re: Color thresholding and obtaining Lab values
> >
> > Yes I did. I just noticed that I can "Restore Selection" after
> > converting the image to Lab stack! So now, I think the following
> > procedure can exclude black and white parts and then apply this
> > selection to Lab stack. This way, I can obtain L, a, b values from
> > only the color-thresholded area. It seems to work, but I would
> > appreciate your comments, as how to get Lab values is not clearly
> explained in the manual.
> >
> > 1. Open --> Open my photo, which is an RGB color image.
> > 2. Image --> Adjust --> Color threshold... --> Set the threshold of L*
> > value to be 71-216 so that the black and white parts will be excluded.
> > --> Select.
> > 3. The yellow parts (of which I want to know the Lab values) are
> > circled with yellow lines now.
> > 4. Edit --> Selection --> Add to manager
> > - in the ROI Manager menus select More --> Multi Measure
> > - in the menu presented, select "Measure all 3 slices" and
> > deselect "One row per slice"
> > 5. Image --> Type --> Lab stack.
> > 6. Edit --> Selection --> Restore selection (The outline of my ROI
> > comes back on the Lab stack images) 7. Plugins -> Stack -> Measure
> > stack
> >
> >
> > Thank you,
> >
> > Rie
> >
> >
> > On 24 May 2018 at 11:59, Straatman, Kees (Dr.) <
[hidden email]>
> > wrote:
> >
> > > Did you do your step 4: > Image --> Type --> Lab stack?
> > >
> > > Kees
> > >
> > > -----Original Message-----
> > > From: Rie Sadohara [mailto:
[hidden email]]
> > > Sent: 24 May 2018 16:58
> > > To:
[hidden email]
> > > Subject: Re: Color thresholding and obtaining Lab values
> > >
> > > Dr. Staatman,
> > >
> > > Thank you for the suggestion. I was able to add the thresholded area
> > > to selection, and it was circled by light blue lines.
> > > However, when I hit Measure, it only gives the area and gray area
> > > values, because it is what is checked in the Analyze -> Set
> > Measurements... option.
> > > There is no L, a, b values to be selected in that option. It seems
> > > that I need to convert the image to Lab stack then hit Measure (or
> > > Plugins -> Stack -> Measure stack) to obtain L, a, and b values. But
> > > when the image is converted to Lab stack, the selection is lost, and
> > > the L, a, b values are based on the entire image including the
> > > portions that I do not want to include.
> > >
> > > I guess my question is: Is it possible to convert the
> > > color-thresholded selection to a Lab stack, or is there a way to
> > > measure L, a, b values without converting the image into Lab stack?
> > >
> > > Kind regards,
> > >
> > > Rie
> > >
> > >
> > >
> > >
> > >
> > >
> > > On 24 May 2018 at 03:24, Straatman, Kees (Dr.)
> > > <
[hidden email]>
> > > wrote:
> > >
> > > > Dear Rie,
> > > >
> > > > To measure only your selection you can use:
> > > > - Edit > Selection > Add to Manager
> > > > - in the ROI Manager menus select More > Multi Measure
> > > > - in the menu presented select "Measure all 3 slices" and deselect
> > > > "One row per slice"
> > > >
> > > > I hope this solves your problem.
> > > >
> > > > Best wishes
> > > >
> > > > Kees
> > > >
> > > >
> > > > Dr Ir K.R. Straatman
> > > > Senior Experimental Officer
> > > > Advanced Imaging Facility
> > > > Centre for Core Biotechnology Services University of Leicester
> > > > www.le.ac.uk/advanced-imaging-facility
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf
> > > > Of Rie Sadohara
> > > > Sent: 22 May 2018 22:13
> > > > To:
[hidden email]
> > > > Subject: Color thresholding and obtaining Lab values
> > > >
> > > > Hello all,
> > > >
> > > > I am trying to get Lab values from images of yellow beans. There
> > > > are some black and white parts in the image, so I want to remove
> > > > those parts and measure the yellowness of the bean seeds. Below
> > > > are the steps I took, but Lab values are calculated from the entire
> image.
> > > > Could someone tell me how to do it right?
> > > >
> > > > 1. Open --> Open my photo, which is an RGB color image.
> > > > 2. Image --> Adjust --> Color threshold... --> Then set the
> > > > threshold of
> > > > L* value to be 71-216 so that the black and white parts will be
> > excluded.
> > > > --> Select.
> > > > 3. The yellow parts (of which I want to know the Lab values) are
> > > > circled with yellow lines now.
> > > > 4. Image --> Type --> Lab stack.
> > > > 5. Analyze --> Measure. for each stack (L, a, and b) 6. The
> > > > returned Lab values are based on the entire image. It works as
> > > > though there had been no color thresholding.
> > > >
> > > > My understanding is that the parts that are circled with bright
> > > > yellow lines after color thresholding are the area that are going
> > > > to be used for Lab measurements? (Please see the attachment. In
> > > > the image, the yellow parts (my ROI) are segregated correctly, but
> > > > how can I get Lab values out of this region?)
> > > >
> > > > Any advice would be greatly appreciated,
> > > >
> > > > Rie
> > > >
> > > >
> > > > --
> > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > > >
> > > > --
> > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > > >
> > >
> > >
> > >
> > > --
> > > ------------------------------------------------------------
> > > ----------------------------------------------------------
> > > *Rie** Sadohara *
> > > Graduate Research Assistant
> > > Department of Plant, Soil and Microbial Sciences Michigan State
> > > University Plant and Soil Science Building
> > > 1066 Bogue St, Room A364
> > > East Lansing, MI 48824
> > > Email: *
[hidden email] <
[hidden email]>* Find
> > > delicious bean recipes here:
> > > *
https://colorfulhealthfulflavorfulblog.wordpress.com/> > > <
https://colorfulhealthfulflavorfulblog.wordpress.com/>*
> > > ------------------------------------------------------------
> > > -------------------
> > > ----------------------------------------
> > >
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> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> >
> >
> >
> > --
> > ------------------------------------------------------------
> > ----------------------------------------------------------
> > *Rie** Sadohara *
> > Graduate Research Assistant
> > Department of Plant, Soil and Microbial Sciences Michigan State
> > University Plant and Soil Science Building
> > 1066 Bogue St, Room A364
> > East Lansing, MI 48824
> > Email: *
[hidden email] <
[hidden email]>* Find
> > delicious bean recipes here:
> > *
https://colorfulhealthfulflavorfulblog.wordpress.com/> > <
https://colorfulhealthfulflavorfulblog.wordpress.com/>*
> > ------------------------------------------------------------
> > -------------------
> > ----------------------------------------
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
>
>
> --
> ------------------------------------------------------------
> ----------------------------------------------------------
> *Rie** Sadohara *
> Graduate Research Assistant
> Department of Plant, Soil and Microbial Sciences Michigan State University
> Plant and Soil Science Building
> 1066 Bogue St, Room A364
> East Lansing, MI 48824
> Email: *
[hidden email] <
[hidden email]>* Find delicious
> bean recipes here:
> *
https://colorfulhealthfulflavorfulblog.wordpress.com/> <
https://colorfulhealthfulflavorfulblog.wordpress.com/>*
> ------------------------------------------------------------
> -------------------
> ----------------------------------------
>
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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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> ImageJ mailing list:
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