diff --git a/napari_segment_blobs_and_things_with_membranes/_bia_bob_plugins.py b/napari_segment_blobs_and_things_with_membranes/_bia_bob_plugins.py new file mode 100644 index 0000000..85e6bc6 --- /dev/null +++ b/napari_segment_blobs_and_things_with_membranes/_bia_bob_plugins.py @@ -0,0 +1,55 @@ +def list_bia_bob_plugins(): + """List of function hints for bia_bob""" + return """ ## napari-segment-blobs-and-things-with-membranes (nsbatwm) + nsbatwm is a Python library that processes images, mostly using the scikit-image library, but with simpler access. + When you use it, you always start by importing the library: `import napari_segment_blobs_and_things_with_membranes as nsbatwm`. + When asked for how to use nsbatwm, you can adapt one of the following code snippets: + + * Splits touching objects in a binary image using an algorithm similar to the ImageJ watershed. + nsbatwm.split_touching_objects(binary_image) + + * Applies Otsu's method to binarize an intensity image (also works with yen, isodata, li, mean, minimum, triangle instead of otsu). + nsbatwm.threshold_otsu(image) + + * Labels connected components in a binary image. + nsbatwm.connected_component_labeling(binary_image) + + * Applies seeded watershed segmentation using labeled objects, e.g. nuclei, and an image showing bright borders between objects such as cell membranes. + nsbatwm.seeded_watershed(image, labeled_objects) + + * Segments blob-like structures using Voronoi-Otsu labeling. + nsbatwm.voronoi_otsu_labeling(image, spot_sigma=4, outline_sigma=1) + + * Applies a Gaussian blur for noise reduction. + nsbatwm.gaussian_blur(image, sigma=5) + + * Applies median filter to reduce noise while preserving edges. + nsbatwm.median_filter(image, radius=5) + + * Smooth a label image using a local most popular intensity (mode) filter. + nsbatwm.mode_filter(labels) + + * Applies a percentile filter. + nsbatwm.percentile_filter(image) + + * Removes background in an image using the top-hat filter. + nsbatwm.white_tophat(image) + + * Applies local minimum filtering to an image (also works with maximum, and mean). + nsbatwm.minimum_filter(image) + + * Subtracts background in an image using the rolling ball algorithm. + nsbatwm.subtract_background(image) + + * Removes labeled objects touching image borders. + nsbatwm.remove_labels_on_edges(label_image) + + * Expands labels by a specified distance. + nsbatwm.expand_labels(label_image, distance=2) + + * Segments using seeded watershed with local minima as seeds. + nsbatwm.local_minima_seeded_watershed(image, spot_sigma=10, outline_sigma=2) + + * Skeletonizes labeled objects. + nsbatwm.skeletonize(image) +""" \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 125f501..e6bb7a4 100644 --- a/setup.cfg +++ b/setup.cfg @@ -45,3 +45,5 @@ install_requires = [options.entry_points] napari.plugin = napari-segment-blobs-and-things-with-membranes = napari_segment_blobs_and_things_with_membranes +bia_bob_plugins = + nsbatwm_plugin = napari_segment_blobs_and_things_with_membranes._bia_bob_plugins:list_bia_bob_plugins \ No newline at end of file