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MorphoDig tutorial 13: reorient, crop and resample µCT data


Drag and drop project file (.NTW) inside main 3D window When opening a NTW file, 3D volumes and 3D surfaces will be unselected by default. To interact with the opened volume, it must be selected first (right click + drag). Selected volumes are drawn with a bounding box. Use the yellow sliders to rotate/translate selected volumes Activate “move selected objects” interaction mode Now use “left click + drag” to rotate the volume, and “middle click + drag” to translate the volume Active “move camera mode” Open the “edit first selected volume” window Click on “display Crop box” button. Adjust the bounds of the crop box (left click + drag the spherical controls) Now click on “crop”. As the volume was rotated, a warning message shows up, indicating that the volume data will be resliced before being cropped Thats it ! Notice that a post fix ( “_rsp_crp”) is added to the name of the volume, to remind us that it was resliced and cropped. Now browse through the re-oriented 2D slices. Modified volume data can be saved inside a new MetaImage (MHD/MHA) file The metaimage (MHD/MHA) format is convenient: it can be used in a wide range of other software, including FIJI Here we compare with FIJI the initial metaimage volume, and the resliced + cropped final volume data.

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