Metadata-Version: 2.2
Name: liffile
Version: 2025.2.8
Summary: Read Leica image files (LIF, LOF, XLIF, XLCF, XLEF, and LIFEXT)
Home-page: https://www.cgohlke.com
Author: Christoph Gohlke
Author-email: cgohlke@cgohlke.com
License: BSD
Project-URL: Bug Tracker, https://github.com/cgohlke/liffile/issues
Project-URL: Source Code, https://github.com/cgohlke/liffile
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: numpy
Provides-Extra: all
Requires-Dist: xarray; extra == "all"
Requires-Dist: tifffile; extra == "all"
Requires-Dist: imagecodecs; extra == "all"
Requires-Dist: matplotlib; extra == "all"
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
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Read Leica image files (LIF, LOF, XLIF, XLCF, XLEF, and LIFEXT)
===============================================================

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), XLEF (XML Experiment File), and LIFEXT (Leica
Image File Extension).

These files are written by LAS X software to store collections of images
and metadata from microscopy experiments.

:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
:License: BSD 3-Clause
:Version: 2025.2.8
:DOI: `10.5281/zenodo.14740657 <https://doi.org/10.5281/zenodo.14740657>`_

Quickstart
----------

Install the liffile package and all dependencies from the
`Python Package Index <https://pypi.org/project/liffile/>`_::

    python -m pip install -U liffile[all]

See `Examples`_ for using the programming interface.

Source code and support are available on
`GitHub <https://github.com/cgohlke/liffile>`_.

Requirements
------------

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

- `CPython <https://www.python.org>`_ 3.10.11, 3.11.9, 3.12.9, 3.13.2 64-bit
- `NumPy <https://pypi.org/project/numpy>`_ 2.2.2
- `Imagecodecs <https://pypi.org/project/imagecodecs>`_ 2024.12.30
  (required for decoding TIFF, JPEG, PNG, and BMP)
- `Xarray <https://pypi.org/project/xarray>`_ 2025.1.2 (recommended)
- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.0 (optional)
- `Tifffile <https://pypi.org/project/tifffile/>`_ 2025.1.10 (optional)

Revisions
---------

2025.2.8

- Support LIFEXT files.
- Remove asrgb parameter from LifImage.asarray (breaking).
- Do not apply BGR correction when using memory block frames.
- Avoid copying single frame to output array.
- Add LifImage.parent_image and child_images properties.
- Add LifImageSeries.find method.

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.

Notes
-----

`Leica Microsystems GmbH <https://www.leica.com/>`_ 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 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 <https://github.com/Arcadia-Science/readlif>`_ and
`Bio-Formats <https://github.com/ome/bioformats>`_ .

Examples
--------

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
