Note
Click here to download the full example code or to run this example in your browser via Binder
Datasets with 3 or more spatial dimensionsΒΆ
Most scikit-image functions are compatible with 3D datasets, i.e., images with
3 spatial dimensions (to be distinguished from 2D multichannel images, which
are also arrays with
three axes). skimage.data.cells3d()
returns a 3D fluorescence microscopy
image of cells. The returned dataset is a 3D multichannel image with dimensions
provided in (z, c, y, x)
order. Channel 0 contains cell membranes, while channel
1 contains nuclei.
The example below shows how to explore this dataset. This 3D image can be used to test the various functions of scikit-image.
Out:
Downloading file 'data/cells3d.tif' from 'https://gitlab.com/scikit-image/data/-/raw/master/cells3d.tif' to '/home/lee8rx/.cache/scikit-image/0.19.2'.
from skimage import data
import plotly
import plotly.express as px
img = data.cells3d()[20:]
fig = px.imshow(img, facet_col=1, animation_frame=0,
binary_string=True, binary_format='jpg')
fig.layout.annotations[0]['text'] = 'Cell membranes'
fig.layout.annotations[1]['text'] = 'Nuclei'
plotly.io.show(fig)
Total running time of the script: ( 0 minutes 3.531 seconds)