BoneJ Analysis of DICOM vs. Bitmap Stacks

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Mark Begonia

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Sep 12, 2015, 3:12:51 PM9/12/15
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Hi everyone,

I have used BoneJ extensively to analyze the area moments of inertia in murine bones. I am usually given DICOM files if the Scanco vivaCT 40 system was used or bitmap files if the Bruker SkyScan 1147 system was used. Recently, I noticed that the units in the Results files are different depending on which type of image stack is analyzed.

For instance, analysis of a DICOM stack yields a volume measurement with units of mm^3. Meanwhile, analysis of a bitmap stack leads to a volume measurement with units of pixels. I do not change anything in the Setup window prior to selecting the moments of inertia option.

Question #1: Is this issue due primarily to the uploading of a bitmap stack?
Question #2: If so, how do I assign the image pixel size?
Question #3: Does it matter when I assign the image pixel size?

If more information is needed in order to answer my initial questions, please let me know.

Sincerely,
Mark

Michael Doube

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Sep 13, 2015, 3:56:24 PM9/13/15
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Hi Mark

> I have used BoneJ extensively to analyze the area moments of inertia

You mean the second moment of area, right?

https://en.wikipedia.org/wiki/Second_moment_of_area
https://en.wikipedia.org/wiki/Moment_of_inertia

> in murine bones. I am usually given DICOM files if the Scanco vivaCT
> 40 system was used or bitmap files if the Bruker SkyScan 1147 system
> was used.

Two points here:

1. BoneJ can also open SCANCO's native file format, if you have those.
2. The SkyScan tomographic reconstruction software can output 16-bit
TIFFs, which I'd strongly encourage you to do.


> For instance, analysis of a DICOM stack yields a volume measurement
> with units of mm^3. Meanwhile, analysis of a bitmap stack leads to a
> volume measurement with units of pixels. I do not change anything in
> the Setup window prior to selecting the moments of inertia option.
>
>
> Question #1: Is this issue due primarily to the uploading of a bitmap
> stack?

Yes - BMPs do not contain any metadata about pixel spacing, greylevel
calibration, specimen data, etc. DICOMs have lots of metadata. TIFF also
has lots of metadata (it stands for Tagged Image File Format), hence my
recommendation to get SkyScan to produce 16-bit TIFFs rather than BMPs.

> Question #2: If so, how do I assign the image pixel size?

Image > Properties

> Question #3: Does it matter when I assign the image pixel size?

Yes. Do it before you do any measuring. Otherwise you have to multiply
your results by pixel spacing afterwards, which will only work if your
pixels are not anisotropically spaced (usually the case in the scanners
you mention).

Best regards,

Michael
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