A pure Python module for visualising 3D segmentation results
Project description
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 3Dnumpy
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 2Dnumpy
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
Project details
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Source Distribution
segview-0.1.1.tar.gz
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