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Color thresholding and obtaining Lab values

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Rie Sadohara

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

Yellow parts are my ROI.jpg (339K) Download Attachment

Joel Sheffield

Re: Color thresholding and obtaining Lab values

How about using Analyze Particles?

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~jbs/>
<http://tinyurl.com/khbouft>*

On Tue, May 22, 2018 at 5:13 PM, Rie Sadohara <[hidden email]>
wrote:

> 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

Re: Color thresholding and obtaining Lab values

Dr. Sheffiled,

Thank you for the suggestion. I have already tried it, but it recognizes
numerous small dots (very very tiny compared to the beans) as particles,
and ignores the beans in the image. I do not know why, but it does not work
as I would like it to.

Rie

On 22 May 2018 at 19:15, Joel Sheffield <[hidden email]> wrote:

> How about using Analyze Particles?
>
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL: *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~jbs/>
> <http://tinyurl.com/khbouft>*
>
> On Tue, May 22, 2018 at 5:13 PM, Rie Sadohara <[hidden email]>
> wrote:
>
> > 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/>*
-------------------------------------------------------------------------------
----------------------------------------

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Joel Sheffield

Re: Color thresholding and obtaining Lab values

You can set a range in Analyze particles to exclude small dots, and even
certain shape parameters. Look at the menu options. Also, consider using
the watershed procedure to isolate specific beans - if that is important to
you.

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL: *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~jbs/>
<http://tinyurl.com/khbouft>*

On Tue, May 22, 2018 at 7:52 PM, Rie Sadohara <[hidden email]>
wrote:

> Dr. Sheffiled,
>
> Thank you for the suggestion. I have already tried it, but it recognizes
> numerous small dots (very very tiny compared to the beans) as particles,
> and ignores the beans in the image. I do not know why, but it does not work
> as I would like it to.
>
> Rie
>
> On 22 May 2018 at 19:15, Joel Sheffield <[hidden email]> wrote:
>
> > How about using Analyze Particles?
> >
> >
> >
> > Joel B. Sheffield, Ph.D
> > Department of Biology
> > Temple University
> > Philadelphia, PA 19122
> > Voice: 215 204 8839
> > e-mail: [hidden email]
> > URL: *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~
> jbs/>
> > <http://tinyurl.com/khbouft>*
> >
> > On Tue, May 22, 2018 at 5:13 PM, Rie Sadohara <[hidden email]>
> > wrote:
> >
> > > 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/>*
> ------------------------------------------------------------
> -------------------
> ----------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Rie Sadohara

Re: Color thresholding and obtaining Lab values

Dr. Sheffield,

Thank you for the suggestion. I have tried analyze particles with different
parameters (size and circularity), but it does not recognize the beans
properly. It seems that this is only effective when the image is a
polka-dot like pattern, where dots are clearly separable from the
background. It is possible that the color thresholding does not work quite
well because "it is not yet fully integrated to ImageJ", according to the
User's Manual. But then why are the beans segregated with the yellow lines
after color-thresholding? it is quite puzzling because it should not be so
hard or complicated to specify which area to use in the image and obtain
Lab values from that area.

On 23 May 2018 at 11:39, Joel Sheffield <[hidden email]> wrote:

> You can set a range in Analyze particles to exclude small dots, and even
> certain shape parameters. Look at the menu options. Also, consider using
> the watershed procedure to isolate specific beans - if that is important to
> you.
>
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL: *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~jbs/>
> <http://tinyurl.com/khbouft>*
>
> On Tue, May 22, 2018 at 7:52 PM, Rie Sadohara <[hidden email]>
> wrote:
>
> > Dr. Sheffiled,
> >
> > Thank you for the suggestion. I have already tried it, but it recognizes
> > numerous small dots (very very tiny compared to the beans) as particles,
> > and ignores the beans in the image. I do not know why, but it does not
> work
> > as I would like it to.
> >
> > Rie
> >
> > On 22 May 2018 at 19:15, Joel Sheffield <[hidden email]> wrote:
> >
> > > How about using Analyze Particles?
> > >
> > >
> > >
> > > Joel B. Sheffield, Ph.D
> > > Department of Biology
> > > Temple University
> > > Philadelphia, PA 19122
> > > Voice: 215 204 8839
> > > e-mail: [hidden email]
> > > URL: *https://bio.cst.temple.edu/~jbs/ <https://bio.cst.temple.edu/~
> > jbs/>
> > > <http://tinyurl.com/khbouft>*
> > >
> > > On Tue, May 22, 2018 at 5:13 PM, Rie Sadohara <[hidden email]>
> > > wrote:
> > >
> > > > 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/>*
> > ------------------------------------------------------------
> > -------------------
> > ----------------------------------------
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

Krs5

Re: Color thresholding and obtaining Lab values

In reply to this post by Rie Sadohara

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

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
>

Krs5

Re: Color thresholding and obtaining Lab values

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/>*
-------------------------------------------------------------------------------
----------------------------------------

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Rie Sadohara

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/>*
> ------------------------------------------------------------
> -------------------
> ----------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

Krs5

Re: Color thresholding and obtaining Lab values

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/>*
> ------------------------------------------------------------
> -------------------
> ----------------------------------------
>
> --
> 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

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/>*
> > ------------------------------------------------------------
> > -------------------
> > ----------------------------------------
> >
> > --
> > 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
>

Krs5

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/>*
> > ------------------------------------------------------------
> > -------------------
> > ----------------------------------------
> >
> > --
> > 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/>*
-------------------------------------------------------------------------------
----------------------------------------

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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Krs5

Re: Color thresholding and obtaining Lab values

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:

--
----------------------------------------------------------------------------------------------------------------------
*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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Rie Sadohara

Re: Color thresholding and obtaining Lab values

Dr. Straatman,

Thank you, both work and I was able to get L, a, b values after color
thresholding. Thank you very much for your help!

Rie

On 29 May 2018 at 04:19, Straatman, Kees (Dr.) <[hidden email]> wrote:

> 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/>*
> > > ------------------------------------------------------------
> > > -------------------
> > > ----------------------------------------
> > >
> > > --
> > > 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/>*
> ------------------------------------------------------------
> -------------------
> ----------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>