pyometiff 0.0.1

Read and Write OME-TIFFs in Python

About

pyometiff is a Python library for reading and writing OME-TIFF files that are compliant with the OME-XML specifications.

Installation

Run the following to install:

pip install pyometiff

Usage

pyometiff exposes two main classes: OMETIFFReader and OMETIFFWriter which you can use to read and write OME TIFF files.

To open a OME-TIFF image you can create an OMETIFFReaderobject and call its .read() method.

import pathlib
from pyometiff import OMETIFFReader
img_fpath = pathlib.Path("/path/to/img.ome.tiff")

reader = OMETIFFReader(fpath=img_fpath)

img_array, metadata, xml_metadata = reader.read()

similarly, to write an OME-TIFF file, we use the OMETIFFWriter class and its .write() method as in the example.

import pathlib
from pyometiff import OMETIFFWriter
output_fpath = pathlib.Path.cwd().joinpath("test_out.ome.tiff")

# a template metadata dict is available at OMETIFFReader._get_metadata_template()

metadata_dict = {
    "PhysicalSizeX" : "0.88",
    "PhysicalSizeXUnit" : "µm",
    "PhysicalSizeY" : "0.88",
    "PhysicalSizeYUnit" : "µm",
    "PhysicalSizeZ" : "3.3",
    "PhysicalSizeZUnit" : "µm",
    "Channels" : {
        "405" : {
            "Name" : "405nm",
            "SamplesPerPixel": 1,
            "ExcitationWavelength": 405.,
            "ExcitationWavelengthUnit": "nm"
        },
        "488" : {
            "Name" : "488nm",
            "SamplesPerPixel": 1,
            "ExcitationWavelength": 488.,
            "ExcitationWavelengthUnit": "nm"
        },
        "638" : {
            "Name" : "638nm",
            "SamplesPerPixel": 1,
            "ExcitationWavelength": 638.,
            "ExcitationWavelengthUnit": "nm"
        },
    }

# our data in npy format
npy_array_data = np.array(shape=(2, 10, 3, 256, 256))
# a string describing the dimension ordering
dimension_order = "ZTCYX"

writer = OMETIFFWriter(
    fpath=output_fpath,
    dimension_order=dimension_order,
    array=npy_array_data,
    metadata=metadata)

writer.write()

Contacts

Author:

Filippo Maria Castelli
[e-mail]
LENS, European Laboratory for Non-linear Spectroscopy
Via Nello Carrara 1
50019 Sesto Fiorentino (FI), Italy