Skip to main content

A pure Python module for visualising 3D segmentation results

Project description


visualise the 3D segmentation result


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

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

Use SegView

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

segview.annotate_label(image, label, axis=-1)  # see the 2D slice with labels along different axes

segview.render_image(image, metadata)  # see the 3D render of an image

segview.render_image(image, metadata, feature)  # see the 3D image with features

segview.annotate_feature(image, label)  # see 2D slice with features
  • 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

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for segview, version 0.3.0
Filename, size File type Python version Upload date Hashes
Filename, size segview-0.3.0-py3-none-any.whl (16.6 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size segview-0.3.0.tar.gz (16.6 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page