Measuring percentage of red green and blue in an ROI

[Mara Wanderer]

Hello,

I am a veterinary student working on a project involving measuring elasticity of lymph nodes in dogs.  I have ultrasound images in both B mode and elastography.  I would like to outline the lymph nodes in the B mode images as the ROI and overlay this onto the corresponding elastography view and then measure the percentage of blue, red and green in the ROI. I haven't been able to figure out how to do this and I couldn't find a similar operation in the archived messages.  If anyone could give me some advice on the best way to go about this, I would greatly appreciate it!

Thanks,

Mara Wanderer, RVT
LSU SVM

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

[G. Esteban Fernandez]

1. Draw a closed ROI.

2. Press Ctrl-T (Command-T on a Mac) to add it to the list of ROIs in the
"ROI manager" window (ROI Manager pops up automatically when you press
Ctrl-T). The ROI will automatically get a numeric name.

3. Select/activate the elastography image and do Image > Color > Split
channels (assuming your red, green and blue are in one image, if not then
skip this step and just open the separate R, G, and B images).

4. Analyze > Set Measurements > Check the "Mean" and "Show label" boxes.

5. Select/activate the R image window.

6. Select the ROI in the ROI Manager window.

7. Press Ctrl-M (Command-M on a Mac) or click Measure in the ROI Manager
(might be under More) to measure the level of Red in the ROI.

8. Repeat 5-7 with G and B. All values will be reported in Results window.

Good luck and let us know if you have more questions!

-Esteban




On Jun 18, 2017 8:10 PM, "Mara Wanderer" <[hidden email]> wrote:

> Hello,
>
> I am a veterinary student working on a project involving measuring
> elasticity of lymph nodes in dogs.  I have ultrasound images in both B mode
> and elastography.  I would like to outline the lymph nodes in the B mode
> images as the ROI and overlay this onto the corresponding elastography view
> and then measure the percentage of blue, red and green in the ROI. I
> haven't been able to figure out how to do this and I couldn't find a
> similar operation in the archived messages.  If anyone could give me some
> advice on the best way to go about this, I would greatly appreciate it!
>
> Thanks,
>
> Mara Wanderer, RVT
> LSU SVM
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Mara Wanderer]

Hi,

(I meant to hit reply all the first time I sent this so trying again)

I think I am on the right track but what I am getting following your
directions is mean gray values for red, green and blue in the ROI for each
split image. What I really need now is to figure out what percentage of the
ROI is red, what percent is green and what percent is blue.  I'm guessing I
need to change something in the "set measurements" window? I tried checking
the area and area fraction boxes but the measurements for area fraction for
each color comes up as 100%. (making the total for the ROI 300%, so
obviously not possible). I'm not really sure what else to try.  Sorry if
this is a stupid question, I'm pretty new at all of this and I don't really
have any background in any sort of programming! I really appreciate any
help.

Thanks,

Mara


On Mon, Jun 19, 2017 at 12:12 AM G. Esteban Fernandez <
[hidden email]> wrote:

> 1. Draw a closed ROI.
>
> 2. Press Ctrl-T (Command-T on a Mac) to add it to the list of ROIs in the
> "ROI manager" window (ROI Manager pops up automatically when you press
> Ctrl-T). The ROI will automatically get a numeric name.
>
> 3. Select/activate the elastography image and do Image > Color > Split
> channels (assuming your red, green and blue are in one image, if not then
> skip this step and just open the separate R, G, and B images).
>
> 4. Analyze > Set Measurements > Check the "Mean" and "Show label" boxes.
>
> 5. Select/activate the R image window.
>
> 6. Select the ROI in the ROI Manager window.
>
> 7. Press Ctrl-M (Command-M on a Mac) or click Measure in the ROI Manager
> (might be under More) to measure the level of Red in the ROI.
>
> 8. Repeat 5-7 with G and B. All values will be reported in Results window.
>
> Good luck and let us know if you have more questions!
>
> -Esteban
>
>
>
>
> On Jun 18, 2017 8:10 PM, "Mara Wanderer" <[hidden email]>
> wrote:
>
>> Hello,
>>
>> I am a veterinary student working on a project involving measuring
>> elasticity of lymph nodes in dogs.  I have ultrasound images in both B mode
>> and elastography.  I would like to outline the lymph nodes in the B mode
>> images as the ROI and overlay this onto the corresponding elastography view
>> and then measure the percentage of blue, red and green in the ROI. I
>> haven't been able to figure out how to do this and I couldn't find a
>> similar operation in the archived messages.  If anyone could give me some
>> advice on the best way to go about this, I would greatly appreciate it!
>>
>> Thanks,
>>
>> Mara Wanderer, RVT
>> LSU SVM
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>

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

[G. Esteban Fernandez]

Hi Mara,

I understand the problem better now.  You need to quantify the percentage
AREA of R, G, and B (not the intensity).  You were on the right track with
thinking you need to use the Area fraction measurement.  Try this:

1. Draw a closed ROI.

2. Press Ctrl-T (Command-T on a Mac) to add it to the list of ROIs in the
"ROI manager" window (ROI Manager pops up automatically when you press
Ctrl-T). The ROI will automatically get a numeric name.

3. Select/activate the elastography image and do Image > Color > Split
channels (assuming your red, green and blue are in one image, if not then
skip this step and just open the separate R, G, and B images).

4. Analyze > Set Measurements > Check the boxes for "Area fraction", "Limit
to threshold", and "Show label".

5. Select/activate the R image window.

6. Press Ctrl-Shift-T (Command-Shift-T on a Mac) to run the "Threshold"
function.

7. In the Threshold window choose "Red" from the second dropdown menu, then
use the sliders to highlight in red the area you want to measure (red is
the arbitrary color that the creators of ImageJ chose as the
highlight/overlay color, it isn't related to the color you're quantifying).
What you're doing is choosing an intensity range that your areas of
interest fall into and the sliders are the lower and upper intensity range;
move them back and forth until only the areas you want are highlighted in
red and background areas are not highlighted.  .

8. Select the ROI in the ROI Manager window.

9. Press Ctrl-M (Command-M on a Mac) or click Measure in the ROI Manager to
measure the area fraction of Red in the ROI.

10. Repeat 5-9 with G and B. All values will be reported in Results window.


-Esteban



On Sun, Jun 25, 2017 at 5:39 PM, Mara Wanderer <[hidden email]>
wrote:

> Hi,
>
> (I meant to hit reply all the first time I sent this so trying again)
>
> I think I am on the right track but what I am getting following your
> directions is mean gray values for red, green and blue in the ROI for each
> split image. What I really need now is to figure out what percentage of the
> ROI is red, what percent is green and what percent is blue.  I'm guessing I
> need to change something in the "set measurements" window? I tried checking
> the area and area fraction boxes but the measurements for area fraction for
> each color comes up as 100%. (making the total for the ROI 300%, so
> obviously not possible). I'm not really sure what else to try.  Sorry if
> this is a stupid question, I'm pretty new at all of this and I don't really
> have any background in any sort of programming! I really appreciate any
> help.
>
> Thanks,
>
> Mara
>
>
> On Mon, Jun 19, 2017 at 12:12 AM G. Esteban Fernandez <
> [hidden email]> wrote:
>
>> 1. Draw a closed ROI.
>>
>> 2. Press Ctrl-T (Command-T on a Mac) to add it to the list of ROIs in the
>> "ROI manager" window (ROI Manager pops up automatically when you press
>> Ctrl-T). The ROI will automatically get a numeric name.
>>
>> 3. Select/activate the elastography image and do Image > Color > Split
>> channels (assuming your red, green and blue are in one image, if not then
>> skip this step and just open the separate R, G, and B images).
>>
>> 4. Analyze > Set Measurements > Check the "Mean" and "Show label" boxes.
>>
>> 5. Select/activate the R image window.
>>
>> 6. Select the ROI in the ROI Manager window.
>>
>> 7. Press Ctrl-M (Command-M on a Mac) or click Measure in the ROI Manager
>> (might be under More) to measure the level of Red in the ROI.
>>
>> 8. Repeat 5-7 with G and B. All values will be reported in Results window.
>>
>> Good luck and let us know if you have more questions!
>>
>> -Esteban
>>
>>
>>
>>
>> On Jun 18, 2017 8:10 PM, "Mara Wanderer" <[hidden email]>
>> wrote:
>>
>>> Hello,
>>>
>>> I am a veterinary student working on a project involving measuring
>>> elasticity of lymph nodes in dogs.  I have ultrasound images in both B mode
>>> and elastography.  I would like to outline the lymph nodes in the B mode
>>> images as the ROI and overlay this onto the corresponding elastography view
>>> and then measure the percentage of blue, red and green in the ROI. I
>>> haven't been able to figure out how to do this and I couldn't find a
>>> similar operation in the archived messages.  If anyone could give me some
>>> advice on the best way to go about this, I would greatly appreciate it!
>>>
>>> Thanks,
>>>
>>> Mara Wanderer, RVT
>>> LSU SVM
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>

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