Liffile is a Python library to read image and metadata from Leica image files: LIF (Leica Image File), LOF (Leica Object File), XLIF (XML Image File), XLCF (XML Collection File), and XLEF (XML Experiment File).
These files are written by LAS X software to store collections of images and metadata from microscopy experiments.
| Author: | Christoph Gohlke |
|---|---|
| License: | BSD 3-Clause |
| Version: | 2025.2.6 |
| DOI: | 10.5281/zenodo.14740657 |
Install the liffile package and all dependencies from the Python Package Index:
python -m pip install -U liffile[all]
See Examples for using the programming interface.
Source code and support are available on GitHub.
This revision was tested with the following requirements and dependencies (other versions may work):
- CPython 3.10.11, 3.11.9, 3.12.9, 3.13.2 64-bit
- NumPy 2.2.2
- Imagecodecs 2024.12.30 (required for decoding TIFF, JPEG, PNG, and BMP)
- Xarray 2025.1.2 (recommended)
- Matplotlib 3.10.0 (optional)
- Tifffile 2025.1.10 (optional)
2025.2.6
- Support XLEF and XLCF files.
- Rename LifFile.series property to images (breaking).
- Rename imread series argument to image (breaking).
- Remove LifImage.index property (breaking).
- Add parent and children properties to LifFile.
- Improve detection of XML codecs.
- Do not keep XML files open.
2025.2.5
- Support XLIF files.
- Revise LifMemoryBlock (breaking).
- Replace LifImage.is_lof property with format (breaking).
- Require imagecodecs for decoding TIF, JPEG, PNG, and BMP frames.
2025.2.2
- Add LifFlimImage class.
- Derive LifImage and LifFlimImage from LifImageABC.
- Rename LifImage.guid property to uuid (breaking).
- Add LifFile.uuid property.
2025.1.31
- Support LOF files.
- Make LifFile.xml_header a function (breaking).
2025.1.30
- Remove LifFile.flim_rawdata (breaking).
- Add index, guid, and xml_element_smd properties to LifImage.
2025.1.26
- Fix image coordinate values.
- Prompt for file name if main is called without arguments.
2025.1.25
- Initial alpha release.
Leica Microsystems GmbH is a manufacturer of microscopes and scientific instruments for the analysis of micro and nanostructures.
This library is in its early stages of development. It is not feature-complete. Large, backwards-incompatible changes may occur between revisions.
Specifically, the following features are currently not supported: XLLF and LIFEXT formats, image mosaics and pyramids, partial image reads, reading non-image data like FLIM/TCSPC, heterogeneous channel data types, discontiguous storage, and bit increments.
The XLIF, XLEF, and XLCF formats may not work on case-sensitive file systems since file names are stored case-insensitive.
The library has been tested with a limited number of version 2 files only.
The Leica image file formats are documented at:
- Leica Image File Formats - LIF, XLEF, XLLF, LOF. Version 3.2. Leica Microsystems GmbH. 21 September 2016.
- Annotations to Leica Image File Formats for LAS X Version 3.x. Version 1.4. Leica Microsystems GmbH. 24 August 2016.
- TSC SP8 FALCON File Format Description. LAS X Version 3.5.0.
Other implementations for reading Leica image files are readlif and Bio-Formats .
Read a FLIM lifetime image and metadata from a LIF file:
>>> with LifFile('tests/data/FLIM.lif') as lif:
... for image in lif.images:
... name = image.name
... image = lif.images['Fast Flim']
... assert image.shape == (1024, 1024)
... assert image.dims == ('Y', 'X')
... lifetimes = image.asxarray()
...
>>> lifetimes
<xarray.DataArray 'Fast Flim' (Y: 1024, X: 1024)> Size: 2MB
array([[...]],
shape=(1024, 1024), dtype=float16)
Coordinates:
* Y (Y) float64... 0.0005564
* X (X) float64... 0.0005564
Attributes...
path: FLIM_testdata.lif/sample1_slice1/FLIM Compressed/Fast Flim
F16: {'Name': 'F16',...
TileScanInfo: {'Tile': {'FieldX': 0,...
ViewerScaling: {'ChannelScalingInfo': {...View the image and metadata in a LIF file from the console:
$ python -m liffile tests/data/FLIM.lif