oiffile 2023.8.30

Read Olympus(r) image files (OIF and OIB)

Oiffile is a Python library to read image and metadata from Olympus Image Format files. OIF is the native file format of the Olympus FluoView(tm) software for confocal microscopy.

There are two variants of the format:

• OIF (Olympus Image File) is a multi-file format that includes a main setting file (.oif) and an associated directory with data and setting files (.tif, .bmp, .txt, .pty, .roi, and .lut).

• OIB (Olympus Image Binary) is a compound document file, storing OIF and associated files within a single file.

Author:

Christoph Gohlke

License:

BSD 3-Clause

Version:

2023.8.30

Quickstart

Install the oiffile package and all dependencies from the Python Package Index:

python -m pip install -U oiffile[all]

View image and metadata stored in a OIF or OIB file:

python -m oiffile file.oif

See Examples for using the programming interface.

Source code and support are available on GitHub.

Requirements

This revision was tested with the following requirements and dependencies (other versions may work):

• CPython 3.9.13, 3.10.11, 3.11.5, 3.12rc, 64-bit

• NumPy 1.25.2

• Tifffile 2023.8.30

Revisions

2023.8.30

• Fix linting issues.

• Add py.typed marker.

• Drop support for Python 3.8 and numpy < 1.22 (NEP29).

2022.9.29

• Switch to Google style docstrings.

2022.2.2

• Add type hints.

• Add main function.

• Add FileSystemAbc abstract base class.

• Remove OifFile.tiffs (breaking).

• Drop support for Python 3.7 and numpy < 1.19 (NEP29).

2021.6.6

• Fix unclosed file warnings.

2020.9.18

• Remove support for Python 3.6 (NEP 29).

• Support os.PathLike file names.

• Fix unclosed files.

2020.1.18

• Fix indentation error.

2020.1.1

• Support multiple image series.

• Parse shape and dtype from settings file.

• Remove support for Python 2.7 and 3.5.

• Update copyright.

Notes

The API is not stable yet and might change between revisions.

No specification document is available.

Tested only with files produced on Olympus FV1000 hardware.

Examples

Read the image from an OIB file as numpy array:

>>> image = imread('test.oib')
>>> image.shape
(3, 256, 256)
>>> image[:, 95, 216]
array([820,  50, 436], dtype=uint16)

Read the image from a single TIFF file in an OIB file:

>>> with OifFile('test.oib') as oib:
...     filename = natural_sorted(oib.glob('*.tif'))[0]
...     image = oib.asarray(filename)
>>> filename
'Storage00001/s_C001.tif'
>>> image[95, 216]
820

Access metadata and the OIB main file:

>>> with OifFile('test.oib') as oib:
...     oib.axes
...     oib.shape
...     oib.dtype
...     dataname = oib.mainfile['File Info']['DataName']
'CYX'
(3, 256, 256)
dtype('uint16')
>>> dataname
'Cell 1 mitoEGFP.oib'

Extract the OIB file content to an OIF file and associated data directory:

>>> import tempfile
>>> tempdir = tempfile.mkdtemp()
>>> oib2oif('test.oib', location=tempdir)
Saving ... done.

Read the image from the extracted OIF file:

>>> image = imread(f'{tempdir}/{dataname[:-4]}.oif')
>>> image[:, 95, 216]
array([820,  50, 436], dtype=uint16)

Read OLE compound file and access the ‘OibInfo.txt’ settings file:

>>> with CompoundFile('test.oib') as com:
...     info = com.open_file('OibInfo.txt')
...     len(com.files())
14
>>> info = SettingsFile(info, 'OibInfo.txt')
>>> info['OibSaveInfo']['Version']
'2.0.0.0'