http://imagej.273.s1.nabble.com/Color-thresholding-and-obtaining-Lab-values-tp5020700p5020735.html
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.
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 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
> 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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Department of Plant, Soil and Microbial Sciences Michigan State University Plant and Soil Science Building