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Bring 3D HREM Datasets Into The Physical Realm With 3D Printing

HREM (High Resolution Episcopic Microscopy) allows for the visualisation of 3D datasets through a series of 2D images. In this article we will discuss the process of turning these virtual stacks into blown up physical models.

Mouse Heart 3D Datasets HREM

1. Take the dataset and process to remove background and Invert. As with any dataset this can be done in Fiji (Image) or through OHREM Utilities (Indigo Scientific). When opening the dataset be sure not to use a virtual stack. It may be a good idea at this point to scale your images as the full resolution will not be needed.

2. In Fiji Create a mask of the inverted image by going through the menu

Process -> Binary -> Convert to Mask

3. Now we must fill in the holes. To do this go to Process -> Binary -> Fill Holes