How can I calculate BV/TV ratio of cranium?

I am a student and research the topic of the critical cranial bone defect.

Now, I am confused with a problem that I used Bone J to calculate the BV/TV ratio of the defect site.

But the data showed higher than I except (I except the negative control will approach to 0%, but I obtain 95%). So I would wonder to know if I set the wrong parameter during the process, or I need to set something new?

This is my setting process:
Specify for a region → Adjust the new Contrast → Duplicate the stack would like to calculate → Set the Threshold to convert Binary → Plugin (→Bone J→Fraction→Area/Volume fraction)

In addition, I also can’t obtain the same total volume after specifying the same region. How to explain this problem? Does the result decide to the head position of Rattus during scanning?

Thanks for the person who resolves my problem. If there has the wrong grammar, please correct to me!

Sincerely,
Jeffrey (Zhen-Jie)

Hi Jeffrey,

I suspect the thresholding didn’t work the way you expected it: it is measuring the black pixels as foreground. When you do “Apply threshold”, make sure you tick the “dark background” box.

You can check if this works on the top of your image - but beware of the lookup table (LUT) - the image in your example has an “inverted lookup table” (see right above your image!) which means that 0-value pixels are shown in white and 255-value pixels are shown in black…

I don’t understand what you mean by “obtain the same total volume” - are you using a region of interest (ROI)? Can you explain further, maybe with an example?

Hope this helps!

Best,
Alessandro

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Hi Alessandrofelder:

I will try the resolvation of the first doubt later.

The second doubt, I try my best to explain in detail.
Because I specify a region(10080*7500 um) on my image and duplicate slides, I can use Bone J to calculate a total volume value.
But when I set the same region and duplicate the same slides to other images, I can’t obtain the same total volume value in each image.
This is the problem I was confused.

Sincerely,
Jeffrey (Zhen-Jie)

Hi Jeffrey,

Great, let us know how it goes

What total volumes do you get? Is the scale the same in both images? Can you share some example data with us so we can reproduce the error?

Thanks and best,
Alessandro

Hi, Alessandrofelder:

I tried the first time, but it still didn’t work. After changing the " Dark " option to " Default " from the windows, I got the value I expect! (Fig. 1)
Can I ask you what means " Default "?

After trying the latest way to calculate my data, I found this problem was resolved! But I still didn’t classify the different slides will change the total volume. (Fig. 2)

If I would like to set a regular value, I need to set the same slides’ number and specify the same range without the same position on the image, Right?
(I mean I use the regular value to create a region and slides’ number but calculate any position I set on the image. I can obtain the same total volume.)

Thanks and best,
Jeffrey (Zhen-Jie)

Hi Jeffrey,

After changing the " Dark " option to " Default " from the windows, I got the value I expect! (Fig. 1)

You’re right! What works for me in all cases, was to change the to “dark” instead of default and ticking the “Black background (of binary masks)” box. I should have tested my explanation above - sorry. I believe if you put “Default” in the “Background” drop-down thingie it can sometimes go wrong, especially if you look at images with ~50% foreground and 50% background (This is just my experience, someone more versed than me can probably explain this better). Although in your images it seems that there is always very little foreground, so your method should always work in practice.

Yes, same size ROI should always give the same total volume. The small difference (5.91 vs 5.66) suggests to me maybe you unintentionally changed the size of the ROI rectangle? Otherwise, I don’t know why this is happening.

Finally, Volume fraction should be calculated in 3D, on an image stack - you are doing that right?

Hope this helps,
Alessandro

Hi, Alessandrofelder

Yes! I dropped my roll data to the software, it seems an image stack.

That’s fine! I appreciate that you explain to me patiently. It helps me a lot!

If I have any problem, can I send the message to you on this website?

Sincerely,
Jeffrey (Zhen-Jie)

1 Like

Hi Jeffrey,

It is better if you post questions here, so other people benefit from our discussion too.

Best,
Alessandro

2 Likes

Hi, Alessandrofelder

Thank you, you really help me a lot.

There is another question that how can I duplicate the region is same as the Specify region which I set?

I set the circle region, but I obtained a square region after duplicating the image. And then, I tried to calculate the Area, the system seemed unlike Image pro can specific calculated the circle region. (Fig. 1)

Sincerely,
Jeffery

Hi Jeffrey,

I am not sure I completely understand your question: the way I understand it, you are right: IJ only has rectangular images, so when you duplicate a circular ROI, you will get a rectangular image with that circle inside it.

However, you can measure the area of the circle:

I have made a circular selection, duplicated it, and then clicked Analyze -> Set Measurements -> ticked the “Area” box and then clicked Analyze -> Measure.

15730 is the result I would expect: (a circle with radius 70 has area 15393.8) whereas the area of the rectangle (141 * 142) is 20022.

Hope this helps!

Alessandro

PS next time, when you have another question, it would be better to put it in a new discussion: it will make it easier to find for others.