segmentation: thresholding method

[Anna]

Dear Michael,

I wanted to get morphometric measurements on trabecular bone (Figure trab attached).

I have selected the trabecular region only and run:

1. plugin>bonej>optimize threshold. the result as Figure trab-1. The bone and background been assigned a value of 0.<- I referred your paper on BoneJ. The result BV/TV=0.09

2. image>adjust>threshold (with dark background checked) as in figure trab-2. The bone is 255 and how I can remove the non-bone region? BV/TV=0.32. Is it possible to get the bone BV/TV by subtracting the value of BV/TV of trab-2 - BV/TV of trab-3 to get the BV/TV of the bone?

3. similar step in (2) but with dark background unchecked as in figure trab-3. the bone and background are 0. BV/TV=0.68

Could you advise me for the above options to get the BV/TV of the trabecular bone?

Many thanks!

best regards,

Anna

[Michael Doube]

Hi Anna,

Draw an ROI as you have done in trab-1.tif and add it to the ROI manager by hitting t on your keyboard. Then select the 'Use ROI Manager' option in Volume Fraction, and only the pixels in the ROI you drew will contribute to the BV/TV measurement.

Be careful about pixel values and look-up tables - default in ImageJ is to use black = 255 and white = 0, where 255 is 'foreground' and 0 is 'background'. BoneJ treats 255 as bone and 0 as non-bone. You can apply any LUT so your human eyes see meaningful colour or shades of grey - to the computer the pixel value is what is important.

Michael

On 21/04/15 20:09, Anna wrote:
> Dear Michael,
>
> I wanted to get morphometric measurements on trabecular bone (Figure trab attached).
>
> I have selected the trabecular region only and run:
>

> 1. plugin>bonej>optimize threshold. the result as Figure trab-1. The bone and background been assigned a value of 0.<- I referred your paper on BoneJ. The result *BV/TV=0.09*
> 2. image>adjust>threshold (with dark background checked) as in figure trab-2. The bone is 255 and how I can remove the non-bone region? *BV/TV=0.32*. Is it possible to get the *bone BV/TV by subtracting the value of BV/TV of trab-2 - BV/TV of trab-3 to get the BV/TV of the bone?*
> 3. similar step in (2) but with dark background unchecked as in figure trab-3. the bone and background are 0.*BV/TV=0.68*

[Shafini Mohamad]

Dear Michael,

Many thanks! 

I've tried it and the bone now is 255 and the background=0. It automatically directed me to change the threshold after boneJ>volume fraction (as in trab-5) the BV/TV=0.09- this value attribute to cortical and trabecular. But could I get only the trabecular?

I've tried one method last night, by select the ROI and then edit>selection>make inverse>>fill (Figure inverse) and then image>threshold as in figure. by doing this i got the background=0 but after I try to segment to get only trabecular, the threshold dialog showed no histogram as in figure inverse (attached).

best regards

Anna

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