Visualize

Data visualization 
# load sample data
data4D = img2float(cells3d())
data = data4D[:, 1, :, :] # load the nuclei channel

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:
plot_image(data[30])

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)
show_multichannel(data4D[35], cmap='gray', layout='multirow', num_cols=1);
(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 
mosaic_image_3d(torch_from_numpy(data), figsize=None)

show_images_grid(data, cmap='gray');

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 
visualize_slices(data, showlines=False)

visualize_slices(data, (25,100,150), linestyle=':')

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 
slice_explorer(data4D, order='ZCYX', title='Cells 3D')

static image of slice explorer

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. 
plot_volume(data[:, 50:150, 50:150])
Unable to display output for mime type(s): application/vnd.plotly.v1+json

static image of interactive 3D plot