CZI manager module

This module takes care of the CZI file management. We used to use the bftool kit (https://www.openmicroscopy.org/) which is a set of Java tools, but we opted to use a pure python library that can handle CZI files. https://github.com/AllenCellModeling/aicspylibczi

class library.image_manipulation.czi_manager.CZIManager(czi_file)

Bases: library.image_manipulation.file_logger.FileLogger

Methods to extract meta-data from czi files using AICSImage module (Allen Institute)

extract_metadata_from_czi_file(czi_file, czi_file_path, debug: bool = False)

This will parse the xml metadata and return the relevant data.

Parameters

• czi_file – string of the CZI file name

• czi_file_path – string of the CZI path

Returns

dictionary of the metadata

get_scene(scene_index, channel, scale=1)

Gets the correct scene from the slide

Parameters

• scene_index – integer of the scene index

• channel – integer of the channel

• scale – integer of the scale. Usually either 1 or 16 (full or downsampled)

Returns

the scene

get_scene_dimension(scene_index)

Gets the bounding box size of the scene

Parameters

scene_index – integer of the scene index

Returns

x,y,width and height of the bounding box

library.image_manipulation.czi_manager.extract_png_from_czi(file_key: tuple, normalize: bool = True)

This method creates a PNG file from the TIFF file. This is used for viewing on a web page.

Parameters

• file_key – tuple of _, infile, outfile, scene_index, scale

• normalize – a boolean that determines if we should normalize the TIFF

library.image_manipulation.czi_manager.extract_tiff_from_czi(file_key: tuple)

Gets the TIFF file out of the CZI and writes it to the filesystem

Parameters

file_key – a tuple of: czi_file, output_path, checksum_filepath, scenei, channel, scale