Working with multi-dimensional images

[1]:
import seaborn_image as isns
from skimage import exposure # for adjusting image exposure
/home/docs/checkouts/readthedocs.org/user_builds/seaborn-image/envs/latest/lib/python3.8/site-packages/traitlets/traitlets.py:3044: FutureWarning: --rc={'figure.dpi': 96} for dict-traits is deprecated in traitlets 5.0. You can pass --rc <key=value> ... multiple times to add items to a dict.
  warn(

Load a sample multi-dimension image array

[2]:
cells = isns.load_image("cells")
cells.shape
[2]:
(256, 256, 60)

Plot specific slices from 3-D data

[3]:
g = isns.ImageGrid(cells, slices=[10,20,30,40,50,55])
../_images/Tutorial_Multi_Dim_Images_5_0.svg

You can apply changes to the entire grid. Here, we hide the colorbar and change the colormap.

[4]:
g = isns.ImageGrid(cells, slices=[10,20,30,40,50,55], cbar=False, cmap="inferno")
../_images/Tutorial_Multi_Dim_Images_7_0.svg

Index along different axis

[5]:
g = isns.ImageGrid(
    cells,
    slices=[10,20,30,40,50,55],
    axis=1,
    cbar=False
)
../_images/Tutorial_Multi_Dim_Images_9_0.svg

Variable step sizes and start/end points

[6]:
g = isns.ImageGrid(
    cells,
    step=3,
    start=10,
    stop=40,
    cbar=False
)
../_images/Tutorial_Multi_Dim_Images_11_0.svg

Variable column length and figure size

Change column length and figure size using the col_wrap and height parameter, respectively

[7]:
g = isns.ImageGrid(cells, cbar=False, height=1, col_wrap=10)
../_images/Tutorial_Multi_Dim_Images_13_0.svg

Map a function to transform the 3-D data

Here, we will adjust the exposure using the adjust_gamma function from scikit-image. This can done by passing the function object to the map_func parameter. Additional parameters to the function object can be passed as kwargs.

[8]:
g = isns.ImageGrid(
    cells,
    map_func=exposure.adjust_gamma,
    map_func_kw={"gamma" : 0.5},
    cbar=False,
    height=1,
    col_wrap=10)
../_images/Tutorial_Multi_Dim_Images_15_0.svg
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