http://imagej.273.s1.nabble.com/Color-thresholding-and-obtaining-Lab-values-tp5020700p5020736.html
Hello Dr. Straatman,
stack conversion deletes currently selected area. If I convert the original
color-thresholding. So, before converting the image into Lab stack, I need
area to manager so that I can use it on the Lab-converted image. Those
a Lab stack image. Does it make sense?
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.
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. -->
3. The yellow parts (of which I want to know the Lab values) are circled
4. Edit --> Selection --> Add to manager
5. Image --> Type --> Lab stack.
6. Edit --> Selection --> Restore selection (The outline of my ROI comes
7. In the ROI Manager menus select More --> Multi Measure
> 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
> > >
> > >
> > > --
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http://imagej.nih.gov/ij/list.html> > >
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> > > 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/>*
> ------------------------------------------------------------
> -------------------
> ----------------------------------------
>
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> ImageJ mailing list:
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> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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