segview 0.1.1

A pure Python module for visualising 3D segmentation results

SegView

visualise the 3D segmentation result

Install

• The most convenient way would be: pip3 install segview
• You can also Include the file segview.py in your project directory

(SegView only support Python 3.5+, because it requires PyQt5)

Use SegView

"""
see the 3D model of labels
"""
segview.render_label(label, metadata, alpha=1)

"""
see the 2D slice of labels and the origional images
drag the yellow line to change z-slice index
"""
segview.annotate_label(image, label)

"""
see the 3D distribution of features
"""
segview.render_labels(label, metadata, alpha=1)

"""
see the 2D distribution of features and the origional image
drag the yellow line to change z-slice index
expand/shrink the blue region to include/exclude features in other z-stacks
"""
segview.render_labels(label, metadata, alpha=1)

• label is a 3D numpy array
  • Usually it is the result of image segmentation, having the same structure
  • Value 0 corresponds to the background
  • Its shape is (x, y, z).
• feature is a 2D numpy array
  • Usually it is the result of intensity maxima locating
  • It is 3D positions, [(x1, y1, z1), (x2, y2, z2), ...]
  • Its shape is (feature_number, 3)
• metadata is a dictionary containing the voxel size
  • It is only used in 3D visualisation, as many z-stack images have lower resolutions along z-axis
  • {'voxel_size_x': 1, 'voxel_size_y': 1, 'voxel_size_z': 1}
• alpha adjusts the brightness of the result