Development Status
- 4 - Beta
Intended Audience
- Science/Research
- Developers
Operating System
- OS Independent
Programming Language
- Python :: 3 :: Only
- Python :: 3.11
- Python :: 3.12
- Python :: 3.13
- Python :: 3.14
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:
- License:
BSD-3-Clause
- Version:
2026.2.8
- DOI:
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 an 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):
Revisions
2026.2.8
Fix code review issues.
2026.1.8
Improve code quality.
2025.12.12
Derive OifFileError from ValueError.
Drop support for Python 3.10.
2025.5.10
Remove doctest command line option.
Support Python 3.14.
2025.1.1
Improve type hints.
Drop support for Python 3.9, support Python 3.13.
2024.5.24
…
Refer to the CHANGES file for older revisions.
Notes
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:
>>> 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'
