lfdfiles 2026.1.14
Laboratory for Fluorescence Dynamics (LFD) file formats
License: BSD-3-Clause
Requires Python: >=3.11

Laboratory for Fluorescence Dynamics (LFD) file formats
=======================================================

Lfdfiles is a Python library and console script for reading, writing,
converting, and viewing many of the proprietary file formats used
to store experimental data and metadata at the
`Laboratory for Fluorescence Dynamics <https://www.lfd.uci.edu/>`_.
For example:

- SimFCS VPL, VPP, JRN, BIN, INT, CYL, REF, BH, BHZ, B64, I64, Z64, R64
- FLIMbox FBD, FBF, FBS.XML
- GLOBALS LIF, ASCII
- CCP4 MAP
- Vaa3D RAW
- Bio-Rad(r) PIC
- ISS Vista IFLI, IFI
- FlimFast FLIF

:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
:License: BSD-3-Clause
:Version: 2026.1.14
:DOI: `10.5281/zenodo.8384166 <https://doi.org/10.5281/zenodo.8384166>`_

Quickstart
----------

Install the lfdfiles package and all dependencies from the
`Python Package Index <https://pypi.org/project/lfdfiles/>`_::

    python -m pip install -U "lfdfiles[all]"

Print the console script usage::

    python -m lfdfiles --help

The lfdfiles library is type annotated and documented via docstrings.

See `Examples`_ for using the programming interface.

Source code and support are available on
`GitHub <https://github.com/cgohlke/lfdfiles>`_.

Requirements
------------

This revision was tested with the following requirements and dependencies
(other versions may work):

- `CPython <https://www.python.org>`_ 3.11.9, 3.12.10, 3.13.11, 3.14.2 64-bit
- `NumPy <https://pypi.org/project/numpy>`_ 2.4.1
- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.1.14 (optional)
- `Fbdfile <https://pypi.org/project/fbdfile>`_ 2026.1.14 (optional)
- `Czifile <https://pypi.org/project/czifile/>`_ 2019.7.2.1 (optional)
- `Oiffile <https://pypi.org/project/oiffile/>`_ 2026.1.8 (optional)
- `Netpbmfile <https://pypi.org/project/netpbmfile/>`_ 2026.1.8 (optional)
- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.8
  (optional, for plotting)
- `Click <https://pypi.python.org/pypi/click>`_ 8.3.1
  (optional, for command line apps)

Revisions
---------

2026.1.14

- Improve code quality.

2025.12.12

- Derive LfdFileError from ValueError.
- Improve code quality.

2025.9.17

- Many breaking changes to FLIMbox functionality (use fbdfile package instead):
- Discourage use of FlimboxFbd, FlimboxFbf, and FlimboxFbs classes.
- Use fbdfile package to implement FlimboxFbd, FlimboxFbf, and FlimboxFbs.
- Remove flimbox_histogram, flimbox_decode, and sflim_decode functions.
- Remove convert_fbd2b64 function and fbd2b64 command line app.
- Remove deprecated SimfcsFbf, and SimfcsFbd classes.
- Remove deprecated simfcsfbd_histogram and simfcsfbd_decode functions.

2025.7.31

- Read variants of SimFCS REF files.
- Drop support for Python 3.10.

2025.5.10

- Mark Cython extension free-threading compatible.
- Remove doctest command line option.
- Support Python 3.14.

2025.3.16

- Replace deprecated tifffile.stripnull function.
- Fix misspelled VistaIfli.header keys.
- Drop support for Python 3.9.

2024.10.24

- …

Refer to the CHANGES file for older revisions.

Notes
-----

The API is not stable yet and might change between revisions.

Python <= 3.10 is no longer supported. 32-bit versions are deprecated.

Many of the LFD file formats are not documented and might change arbitrarily.
This implementation is mostly based on reverse engineering existing files.
No guarantee can be made as to the correctness of code and documentation.

Experimental data are often stored in plain binary files with metadata
available in separate, human readable journal files (`.jrn`).

Unless specified otherwise, data are stored in little-endian, C contiguous
order.

The Laboratory for Fluorescence Dynamics (LFD) was a national research
resource center for biomedical fluorescence spectroscopy funded by the
National Institutes of Health from 1986 to 2022 (grant P41GM103540).

References
----------

The following software is referenced in this module:

1.  `SimFCS <https://www.lfd.uci.edu/globals/>`_, a.k.a. Globals for
    Images, is software for fluorescence image acquisition, analysis, and
    simulation, developed by Enrico Gratton at UCI.
2.  `Globals <https://www.lfd.uci.edu/globals/>`_, a.k.a. Globals for
    Spectroscopy, is software for the analysis of multiple files from
    fluorescence spectroscopy, developed by Enrico Gratton at UIUC and UCI.
3.  ImObj is software for image analysis, developed by LFD at UIUC.
    Implemented on Win16.
4.  `FlimFast <https://www.cgohlke.com/flimfast/>`_ is software for
    frequency-domain, full-field, fluorescence lifetime imaging at video
    rate, developed by Christoph Gohlke at UIUC.
5.  `FLImage <https://www.cgohlke.com/#software>`_ is software for
    frequency-domain, full-field, fluorescence lifetime imaging, developed
    by Christoph Gohlke at UIUC. Implemented in LabVIEW.
6.  FLIez is software for frequency-domain, full-field, fluorescence
    lifetime imaging, developed by Glen Redford at UIUC.
7.  Flie is software for frequency-domain, full-field, fluorescence
    lifetime imaging, developed by Peter Schneider at MPIBPC.
    Implemented on a Sun UltraSPARC.
8.  `FLOP97 <https://www.cgohlke.com/#software>`__ is software for
    frequency-domain, cuvette, fluorescence lifetime measurements, developed
    by Christoph Gohlke at MPIBPC. Implemented in LabVIEW.
9.  `VistaVision <http://www.iss.com/microscopy/software/vistavision.html>`_
    is commercial software for instrument control, data acquisition and data
    processing by ISS Inc (Champaign, IL).
10. `Vaa3D <https://github.com/Vaa3D>`_ is software for multi-dimensional
    data visualization and analysis, developed by the Hanchuan Peng group at
    the Allen Institute.
11. `Voxx <https://voxx.sitehost.iu.edu/>`_ is a volume rendering program
    for 3D microscopy, developed by Jeff Clendenon et al. at the Indiana
    University.
12. `CCP4 <https://www.ccp4.ac.uk/>`_, the Collaborative Computational Project
    No. 4, is software for macromolecular X-Ray crystallography.

Examples
--------

Create a Bio-Rad PIC file from a NumPy array:

>>> data = numpy.arange(1000000).reshape((100, 100, 100)).astype('u1')
>>> bioradpic_write('_biorad.pic', data)

Read the volume data from the PIC file as NumPy array, and access metadata:

>>> with BioradPic('_biorad.pic') as f:
...     f.shape
...     f.spacing
...     data = f.asarray()
...
(100, 100, 100)
(1.0, 1.0, 1.0)

Convert the PIC file to a compressed TIFF file:

>>> with BioradPic('_biorad.pic') as f:
...     f.totiff('_biorad.tif', compression='zlib')
...