WrPlot (Wenrui Plot)

Functions of Wenrui to plot. XD

Installation

pip install git+https://github.com/wuwenrui555/wrplot.git

Functions

utils module

• ax_plot_legend(): plot a legend on a matplotlib axes.

• ax_plot_rgb_with_scalebar(): plot a RGB image with a scale bar on a matplotlib axes.

• display_items(): display a list in tabular format.

multiplex module

• create_rgb_multiplex(): convert a multi-channel fluorescence image to a RGB image.

segmentation module

• find_segmentation_boundaries(): convert a segmentation mask to a mask for boundaries.

• ax_plot_segmentation_labels(): plot segmentation labels on a matplotlib axes.

• create_rgb_annotation(): convert a segmentation mask and annotation information to a phenotype map of RGB image.

geojson module

• ax_plot_geojson_polygon(): plot polygons from a geojson file on a matplotlib axes.

io.tiff module

• TiffZarrReader(): a class to read a large TIFF image using zarr.
• PyramidWriter(): a class to write a multi-resolution image pyramid to a TIFF file.

Tutorials

• Multiplex

• Segmentation Mask and Phenotype Map