spacr.measure¶
Module Contents¶
- spacr.measure.get_components(cell_mask, nucleus_mask, pathogen_mask)[source]¶
Get the components (nucleus and pathogens) for each cell in the given masks.
- Parameters:
cell_mask (ndarray) – Binary mask of cell labels.
nucleus_mask (ndarray) – Binary mask of nucleus labels.
pathogen_mask (ndarray) – Binary mask of pathogen labels.
- Returns:
- A tuple containing two dataframes - nucleus_df and pathogen_df.
- nucleus_df (DataFrame): Dataframe with columns ‘cell_id’ and ‘nucleus’,
representing the mapping of each cell to its nucleus.
- pathogen_df (DataFrame): Dataframe with columns ‘cell_id’ and ‘pathogen’,
representing the mapping of each cell to its pathogens.
- Return type:
tuple
- spacr.measure.save_and_add_image_to_grid(png_channels, img_path, grid, plot=False)[source]¶
Add an image to a grid and save it as PNG.
- Parameters:
png_channels (ndarray) – The array representing the image channels.
img_path (str) – The path to save the image as PNG.
grid (list) – The grid of images to be plotted later.
- Returns:
Updated grid with the new image added.
- Return type:
grid (list)
- spacr.measure.img_list_to_grid(grid, titles=None)[source]¶
Plot a grid of images with optional titles.
- Parameters:
grid (list) – List of images to be plotted.
titles (list) – List of titles for the images.
- Returns:
The matplotlib figure object containing the image grid.
- Return type:
fig (Figure)
- spacr.measure.measure_crop(settings)[source]¶
Measure the crop of an image based on the provided settings.
- Parameters:
settings (dict) – The settings for measuring the crop.
- Returns:
None