Visualization

The qim3d library allows for quick and easy visualization of volumetric data. First, qim3d is imported, and a mussel volume is loaded:

import qim3d
downloader = qim3d.io.Downloader()
volume = downloader.Mussel.ClosedMussel1_DOWNSAMPLED(load_file=True)

Slices

Equidistant slices of the mussel µCT-scan can be viewed. Here 15 slices are chosen:

qim3d.viz.slices_grid(volume, num_slices=15, color_map='Blues')

One can interactively scroll through the different axes of the volume:

qim3d.viz.slicer_orthogonal(volume, colormap='Blues')

Histogram

Histograms of the voxel intensities from a volume can help detect possible segmentation thresholds. The coarseness parameter is used to subsample the original volume to get a quick estimate:

qim3d.viz.histogram(volume, bins=100, coarseness=2)

Subsampled volume has size 12.5% of the original volume.