Quickstart

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

python -m pip install -U "oiffile[all]"

See Examples and Documentation 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 3.12.10, 3.13.16, 3.14.8, 3.15.0 64-bit

• Numpy 2.5.4

• Tifffile 2026.10.15

Revisions

2026.10.15

• Return image data in axes order and shape of mainfile (#2, breaking).

• Fix image planes lost due to misparsed file names.

• Fix path traversal in OibFileSystem.saveas_oif.

• Fix OifFileSystem.open_file reading files outside of dataset.

• Fix thread-safety of CompoundFile.

• Raise OifFileError on truncated CompoundFile streams.

• Fix infinite loop on cyclic sector chains in CompoundFile.

• Fix OifFile.glob matching.

• Support line scans.

• Require tifffile 2026.10.15.

• Drop support for Python 3.11 and numpy 2.0 (SPEC0).

• Support Python 3.15.

2026.2.8

• Fix code review issues.

2026.1.8

• …

Refer to the CHANGES file for older revisions.

Notes

No specification document is available.

Tested only with files produced on Olympus FV1000 hardware.

Examples

Import functions and classes used in these examples:

>>> from oiffile import CompoundFile, OifFile, SettingsFile, imread, oib2oif

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:

>>> from tifffile import natural_sorted
>>> with OifFile('test.oib') as oib:
...     filename = natural_sorted(oib.glob('*.tif'))[0]
...     image = oib.asarray(filename)
...
>>> filename
'Storage00001/s_C001.tif'
>>> print(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'

Preview image and metadata stored in an OIF or OIB file from the console:

python -m oiffile test.oif