import images 3D stack: how to set original value and resolution

[Nicole Chen]

Hello,

I am doing 3D reconstruction from 2D serial sectioning images. I am confused about the setting of origin and resolution in the filter "Import images (3D stack)". How can I make a 3D model with the correct scale? 

For origin setting in the filter, should I input the original scale there? pixel value for resolution?

Thanks for your reply!

BR, Nicole 

[Michael Jackson]

Yes, if you know the original spacing in units/pixel, then that value goes into the “Resolution” parameter. If you want the 3D Stack to be a specific location in 3D space, you can set the Origin to your liking. This is useful if you are wanting to try and overlay the serial sectioning data with something like a CT scan.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

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[dream3d-users]

Thanks for your reply, Mike!

Could you help me with an example of the resolution setting？ I want to make sure that I understand correctly.

So, here I provide an image, the original pixel value is 1454 * 1454 (and there is a scale bar), I have 50 slice, the thickness between each slice is 8 um. 

How should I input for resolution?

Thank you very much!

BR, Nicole

[Michael Jackson]

Dear Nicole,

   If the only information you have is the scalar bar from the image then you will need to take the image into some sort of image editor and measure, in pixels, the size of the scalar bar. For instance, when I did this for your image I get about 46pixels as the width of the scalar bar. So we have 50um / 46 pixels = 1.1um/pixel. So in the user interface for the “Image Images (3D Stack)” I would put as the “spacing/resolution” values of 1.1, 1.1, 8.0.

Typically the technician who acquired the images should have the proper scaling/resolution values or sometimes they are embedded in a tiff file as meta data.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

To view this discussion on the web visit https://groups.google.com/d/msgid/dream3d-users/1fb2a841-9458-40f4-a607-265b36667db2n%40googlegroups.com.