# load sample data
= img2float(cells3d())
data4D = data4D[:, 1, :, :] # load the nuclei channel data
Visualize
Display 2D images
Function to quickly display 2D images
plot_image
plot_image (values)
Plot a 2D image or the central slice of a 3D image using Matplotlib. The function assumes that ‘values’ is a 2D or 3D array representing an image, typically in grayscale.
Details | |
---|---|
values | A 2D or 3D array of pixel values representing the image. |
# Example usage:
30]) plot_image(data[
plot_image(data)
Display Multichannel images
Function to display RGB and multichannel images
show_multichannel
show_multichannel (img, ax=None, figsize=None, title=None, max_slices=3, ctx=None, layout='horizontal', num_cols=3, cmap=None, norm=None, aspect=None, interpolation=None, alpha=None, vmin=None, vmax=None, origin=None, extent=None, interpolation_stage=None, filternorm=True, filterrad=4.0, resample=None, url=None, data=None, **kwargs)
Show multi-channel CYX image with options for horizontal, square, or multi-row layout.
Type | Default | Details | |
---|---|---|---|
img | A tensor or numpy array representing a multi-channel image. | ||
ax | NoneType | None | The Matplotlib axis to use for plotting. |
figsize | NoneType | None | The size of the figure. |
title | NoneType | None | The title of the image. |
max_slices | int | 3 | The maximum number of slices to display. |
ctx | NoneType | None | The context to use for plotting. |
layout | str | horizontal | The layout type: ‘horizontal’, ‘square’, or ‘multirow’. |
num_cols | int | 3 | The number of columns for the ‘multirow’ layout. Ignored for other layouts. |
cmap | NoneType | None | |
norm | NoneType | None | |
aspect | NoneType | None | |
interpolation | NoneType | None | |
alpha | NoneType | None | |
vmin | NoneType | None | |
vmax | NoneType | None | |
origin | NoneType | None | |
extent | NoneType | None | |
interpolation_stage | NoneType | None | |
filternorm | bool | True | |
filterrad | float | 4.0 | |
resample | NoneType | None | |
url | NoneType | None | |
data | NoneType | None | |
kwargs |
print(data4D[35].shape)
35], cmap='gray', layout='multirow', num_cols=1); show_multichannel(data4D[
(2, 256, 256)
Display 3D images
Function to display 3D images
mosaic_image_3d
mosaic_image_3d (t:(<class'numpy.ndarray'>,<class'torch.Tensor'>), axis:int=0, figsize:tuple=(15, 15), cmap:str='gray', nrow:int=10, alpha=1.0, return_grid=False, add_to_existing=False, **kwargs)
Plots 2D slices of a 3D image alongside a prior specified axis.
Type | Default | Details | |
---|---|---|---|
t | (<class ‘numpy.ndarray’>, <class ‘torch.Tensor’>) | 3D image to plot | |
axis | int | 0 | axis to split 3D array to 2D images |
figsize | tuple | (15, 15) | size of the figure |
cmap | str | gray | colormap to use |
nrow | int | 10 | number of images per row |
alpha | float | 1.0 | transparency of the image |
return_grid | bool | False | return the grid for further processing |
add_to_existing | bool | False | add to existing figure |
kwargs |
show_images_grid
show_images_grid (images, ax=None, ncols=10, figsize=None, title=None, spacing=0.02, max_slices=3, ctx=None, cmap=None, norm=None, aspect=None, interpolation=None, alpha=None, vmin=None, vmax=None, origin=None, extent=None, interpolation_stage=None, filternorm=True, filterrad=4.0, resample=None, url=None, data=None, **kwargs)
Show a list of images arranged in a grid.
Returns: - axes: matplotlib axes containing the grid of images.
Type | Default | Details | |
---|---|---|---|
images | A list of images to display. | ||
ax | NoneType | None | The Matplotlib axis to use for plotting. |
ncols | int | 10 | The number of columns in the grid. |
figsize | NoneType | None | The size of the figure. |
title | NoneType | None | The title of the image. |
spacing | float | 0.02 | The spacing between subplots. |
max_slices | int | 3 | The maximum number of slices to display. |
ctx | NoneType | None | The context to use for plotting. |
cmap | NoneType | None | |
norm | NoneType | None | |
aspect | NoneType | None | |
interpolation | NoneType | None | |
alpha | NoneType | None | |
vmin | NoneType | None | |
vmax | NoneType | None | |
origin | NoneType | None | |
extent | NoneType | None | |
interpolation_stage | NoneType | None | |
filternorm | bool | True | |
filterrad | float | 4.0 | |
resample | NoneType | None | |
url | NoneType | None | |
data | NoneType | None | |
kwargs |
=None) mosaic_image_3d(torch_from_numpy(data), figsize
='gray'); show_images_grid(data, cmap
Show slices
show_plane
show_plane (ax, plane, cmap='gray', title=None, lines=None, linestyle='--', linecolor='white')
Display a slice of the image tensor on a given axis with optional dashed lines.
Type | Default | Details | |
---|---|---|---|
ax | The axis object to display the slice on. | ||
plane | A 2D numpy array representing the slice of the image tensor. | ||
cmap | str | gray | Colormap to use for displaying the image. |
title | NoneType | None | Title for the plot. |
lines | NoneType | None | A list of indices where dashed lines should be drawn on the plane. |
linestyle | str | – | The style of the dashed lines. |
linecolor | str | white | The color of the dashed lines. |
visualize_slices
visualize_slices (data, planes=None, showlines=True, **kwargs)
Visualize slices of a 3D image tensor along its planes, rows, and columns.
Type | Default | Details | |
---|---|---|---|
data | A 3D numpy array representing the image tensor. | ||
planes | NoneType | None | A tuple containing the indices of the planes to visualize. |
showlines | bool | True | Whether to show dashed lines on the planes, rows, and columns. |
kwargs |
=False) visualize_slices(data, showlines
25,100,150), linestyle=':') visualize_slices(data, (
slice_explorer
slice_explorer (data, order='CZYX', **kwargs)
Visualizes the provided data using Plotly’s interactive imshow function with animation support.
Type | Default | Details | |
---|---|---|---|
data | A 3D numpy array representing the image tensor. | ||
order | str | CZYX | The order of dimensions in the data. |
kwargs |
='ZCYX', title='Cells 3D') slice_explorer(data4D, order
plot_volume
plot_volume (values, opacity=0.1, min=0.1, max=0.8, surface_count=5, width=800, height=600)
Interactive visualization of a 3D volume using Plotly. The function assumes that ‘values’ is a 3D array representing the volume data.
Type | Default | Details | |
---|---|---|---|
values | A 3D array of pixel values representing the volume. | ||
opacity | float | 0.1 | Opacity level for the surfaces in the volume plot. |
min | float | 0.1 | Minimum threshold multiplier for the visualization. |
max | float | 0.8 | Maximum threshold multiplier for the visualization. |
surface_count | int | 5 | Number of surfaces to display in the volume plot. |
width | int | 800 | Width of the plotted figure. |
height | int | 600 | Height of the plotted figure. |
50:150, 50:150]) plot_volume(data[:,
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