API#

Read#

`read_czi`(path[, chunk_size, channels, ...])	Read .czi to Image2DModel
`read_openslide`(path[, chunk_size, pyramidal])	Read WSI to Image2DModel
`read_custom`(path[, imread])	Read a custom image file to Image2DModel

Automatically extract a controlled vocabulary of image metadata.

read_metadata(path, image_type[, parse_metadata])

Parse relevant microscopy metadata of dvp-io supported image file

`read_lmd`(path, calibration_points_image[, ...])	Read and parse LMD-formatted masks for the use in spatialdata
`transform_shapes`(shapes, ...[, precision, ...])	Apply coordinate transformation to shapes based on calibration points from a target and a source

`available_reader`([reader_type])	Get a list of all available readers, as provided by alphabase
`parse_df`(df[, obs_index, var_index])	Warning: This function is deprecated and will be removed in the next minor release
`read_precursor_table`(path, reader_type, *[, ...])	Warning: This function is experimental and may change in future versions
`read_pg_table`(path, search_engine, *[, ...])	Read protein group table to the `anndata.AnnData` format

write_lmd(path, annotation, calibration_points)

Write cell annotations to Leica-compatible .xml file