imctools.io¶

imctools.io.utils¶

reshape_long_2_cyx(data, is_sorted=True, shape=None, channel_indices=None)¶

Reshape data from long format into cyx format (channels, y, x).

Parameters

data¶ (memmap) – Input data.
is_sorted¶ (bool) – Whether data are sorted.
shape¶ (Optional[ndarray]) – Custom data shape.
channel_indices¶ (Optional[Sequence[int]]) – Channel indices.

get_ome_xml(img, image_name, channel_names, big_endian, pixel_size, pixel_depth, creator=None, acquisition_date=None, channel_fluors=None, xml_metadata=None, **ome_xml_kwargs)¶

Helper function for xtiff library to get a proper OME-TIFF XML

Return type: ElementTree

sort_acquisition_channels(session)¶: Sort entries of acquisition channels dictionary by channel order number

imctools.io.imc¶

class ImcParser(input_dir)¶

IMC folder parser.

property origin¶

property session¶

get_mcd_xml()¶: Original (raw) metadata from MCD file in XML format.

get_acquisition_data(acquisition_id)¶: Returns AcquisitionData object with binary image data

class ImcWriter(root_output_folder, mcd_parser, txt_acquisitions_map=None, parse_txt=False)¶

Write IMC session data to IMC folder structure.

property folder_name¶

write_imc_folder(create_zip=True, remove_folder=None)¶

imctools.io.mcd¶

class McdParser(filepath, file_handle=None, xml_metadata_filepath=None)¶

Raw MCD file parser.

The McdParser object should be closed using the close method.

property origin¶

property session¶

get_mcd_xml()¶: Original (raw) metadata from MCD file in XML format.

property mcd_filename¶: Name of the open MCD file

get_acquisition_data(acquisition_id)¶: Returns AcquisitionData object with binary image data for given acquisition ID

get_slide_image(slide_id)¶: Get slide image as numpy array

save_slide_image(slide_id, output_folder, output_filename=None)¶: Save slide image

get_panorama_image(panorama_id)¶: Get panorama image as numpy array

save_panorama_image(panorama_id, output_folder, output_filename=None)¶: Save panorama image of the acquisition

get_before_ablation_image(acquisition_id)¶

save_before_ablation_image(acquisition_id, output_folder, output_filename=None)¶

get_after_ablation_image(acquisition_id)¶

save_after_ablation_image(acquisition_id, output_folder, output_filename=None)¶

close()¶: Close file handlers.

class McdXmlParser(mcd_xml, source_path, process_namespaces=False)¶

Converts MCD XML structure into IMC session format.

property origin¶: Origin of the data

property session¶: Root session data

get_mcd_xml()¶: Original (raw) metadata from MCD file in XML format.

Definitions of MCD XML keywords

imctools.io.ometiff¶

class OmeTiffParser(filepath, slide_id=0, channel_id_offset=0)¶

Parser of MCD compatible .OME-TIFF files.

Allows to get a single IMC acquisition from a single OME-TIFF file.

property origin¶

property filepath¶

get_mcd_xml()¶

Original (raw) metadata from MCD file in XML format.

Return type: Optional[str]

get_acquisition_data()¶: Returns AcquisitionData object with binary image data

static extract_acquisition_id(filepath)¶

Extract acquisition ID from source OME-TIFF filepath.

Filename should end with a numeric symbol!

Parameters: filepath¶ (Union[str, Path]) – Input OME-TIFF filepath

imctools.io.txt¶

class TxtParser(filepath, slide_id=0, channel_id_offset=0)¶

Parser of MCD compatible .txt files.

Allows to get a single IMC acquisition from a single TXT file.

property origin¶

property filepath¶

get_acquisition_data()¶: Returns AcquisitionData object with binary image data

static extract_acquisition_id(filepath)¶

Extract acquisition ID from source TXT filepath.

Filename should end with a numeric symbol!

Parameters: filepath¶ (Union[str, Path]) – Input TXT filepath.