Segmentation plot
Functions to visualize segmentation results.
Visualize segmented instances:
Compare segmented instances with a ground truth:
- bigfish.plot.plot_segmentation(image, mask, rescale=False, contrast=False, title=None, framesize=(15, 10), remove_frame=True, path_output=None, ext='png', show=True)
Plot result of a 2-d segmentation, with labelled instances if available.
- Parameters:
- imagenp.ndarray
A 2-d image with shape (y, x).
- masknp.ndarray
A 2-d image with shape (y, x).
- rescalebool, default=False
Rescale pixel values of the image (made by default in matplotlib).
- contrastbool, default=False
Contrast image.
- titlestr, optional
Title of the image.
- framesizetuple, default=(15, 10)
Size of the frame used to plot with
plt.figure(figsize=framesize).- remove_framebool, default=True
Remove axes and frame.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.
- bigfish.plot.plot_segmentation_boundary(image, cell_label=None, nuc_label=None, boundary_size=1, rescale=False, contrast=False, title=None, framesize=(10, 10), remove_frame=True, path_output=None, ext='png', show=True)
Plot the boundary of the segmented objects.
- Parameters:
- imagenp.ndarray
A 2-d image with shape (y, x).
- cell_labelnp.ndarray, optional
A 2-d image with shape (y, x).
- nuc_labelnp.ndarray, optional
A 2-d image with shape (y, x).
- boundary_sizeint, default=1
Width of the cell and nucleus boundaries, in pixel.
- rescalebool, default=False
Rescale pixel values of the image (made by default in matplotlib).
- contrastbool, default=False
Contrast image.
- titlestr, optional
Title of the image.
- framesizetuple, default=(10, 10)
Size of the frame used to plot with
plt.figure(figsize=framesize).- remove_framebool, default=True
Remove axes and frame.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.
- bigfish.plot.plot_segmentation_diff(image, mask_pred, mask_gt, rescale=False, contrast=False, title=None, framesize=(15, 10), remove_frame=True, path_output=None, ext='png', show=True)
Plot segmentation results along with ground truth to compare.
- Parameters:
- imagenp.ndarray
Image with shape (y, x).
- mask_prednp.ndarray
Image with shape (y, x).
- mask_gtnp.ndarray
Image with shape (y, x).
- rescalebool, default=False
Rescale pixel values of the image (made by default in matplotlib).
- contrastbool, default=False
Contrast image.
- titlestr, optional
Title of the plot.
- framesizetuple, default=(15, 10)
Size of the frame used to plot with
plt.figure(figsize=framesize).- remove_framebool, default=True
Remove axes and frame.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.