stackview 0.1.0

Interactive image stack viewing in jupyter notebooks

stackview

Interactive image stack viewing in jupyter notebooks based on numpy_image_widget and ipywidgets.

Installation

pip install stackview

Usage

You can use stackview from within jupyter notebooks as shown below. Also check out the demo notebook on google colab

Starting point is a 3D image dataset provided as numpy array.

from skimage.io import imread
image = imread('data/Haase_MRT_tfl3d1.tif', plugin='tifffile')

You can then view it slice-by-slice:

stackview.slice(image, continuous_update=True)

Orthogonal views are also available:

stackview.orthogonal(image, continuous_update=True)

Furthermore, to visualize an original image in combination with a processed version, a curtain view may be helpful:

stackview.curtain(image, modified_image * 65537, continuous_update=True)

Contributing

Contributions, bug-reports and ideas for further development are very welcome.

License

Distributed under the terms of the BSD-3 license, "stackview" is free and open source software

Issues

If you encounter any problems, please create a thread on image.sc along with a detailed description and tag @haesleinhuepf.