Segment Image Series¶

This function uses watershed segmentation to label individual objects in a series of images.

plantcv.segment_image_series(imgs_paths, masks_paths, rois, save_labels=True, ksize=3)

returns out_labels

• Parameters:

  • imgs_paths = List of paths to the images in the time series. Ordered by time
  • masks_paths = List of paths to the masks in the time series. Each mask should correspond to the image in imgs_paths for the same index
  • rois = List of roi contours
  • save_labels = Optional, saves the labels of each image independently (default: True)
  • ksize = Size of the block in the time dimension to propagate the labels (default: 3)

• Context:

  • Used to obtain individual masks for objects, like full plants or leaves, that grow in a time series of images from being separated to touching

Early time point and corresponding mask

Later time point and corresponding mask

from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file), or "plot" (Jupyter Notebooks or X11)
pcv.params.debug = "print"

# Using segment image series
analysis_image = pcv.segment_image_series(imgs_paths=paths_to_imgs_list, masks_paths=paths_to_masks_list, rois=valid_rois, save_labels=True, ksize=3)

Image Series Segmentation

Source Code: Here