Quickstart

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

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

Print the console script usage:

python -m lfdfiles --help

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 2026.9.20

• Matplotlib 3.11.2 (optional, for plotting)

• Click 8.5.0 (optional, for command line apps)

Revisions

2026.10.15

• Improve reading ISS IFI files.

• Use struct.unpack_from where possible.

• Fix reading big-endian CCP4 map headers.

• Fix convert CLI passing unsupported compress argument to TiffWriter.

• Warn about trailing bytes in ISS IFI files.

2026.6.24

• Add VistaTdflim class for reading ISS Vista TDFLIM files.

• Support Python 3.15.

2026.4.30

• Remove FlimboxFbd, FlimboxFbf, and FlimboxFbs (breaking; use fbdfile).

• Remove CziFile, NetpbmFile, OifFile, and TiffFile wrappers (breaking).

• Add typed __init__ overrides to subclasses with class-specific parameters.

• Drop support for numpy 2.0 (SPEC0).

2026.3.18

• Replace LfdFileRegistry metaclass with __init_subclass__.

• Add LfdFile.open classmethod as typed factory for auto-detection.

• Add LfdFile._probe classmethod for cheap file pre-screening.

• Add asarray overrides with typed signatures to select subclasses.

• Convert _components to classmethod.

• Drop support for Python 3.11.

2026.1.14

• …

Refer to the CHANGES file for older revisions.

Notes

The API is not stable yet and might change between revisions.

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 FLIMbox functionality has been moved to the fbdfile package.

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, a.k.a. Globals for Images, is software for fluorescence image acquisition, analysis, and simulation, developed by Enrico Gratton at UCI.

2. 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 is software for frequency-domain, full-field, fluorescence lifetime imaging at video rate, developed by Christoph Gohlke at UIUC.

5. FLImage 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 is software for frequency-domain, cuvette, fluorescence lifetime measurements, developed by Christoph Gohlke at MPIBPC. Implemented in LabVIEW.

9. VistaVision is commercial software for instrument control, data acquisition and data processing by ISS Inc (Champaign, IL).

10. Vaa3D is software for multi-dimensional data visualization and analysis, developed by the Hanchuan Peng group at the Allen Institute.

11. Voxx is a volume rendering program for 3D microscopy, developed by Jeff Clendenon et al. at the Indiana University.

12. CCP4, 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(TEMP / '_biorad.pic', data)

Read the volume data from the PIC file as NumPy array, and access metadata:

>>> with BioradPic(TEMP / '_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(TEMP / '_biorad.pic') as f:
...     f.totiff(TEMP / '_biorad.tif', compression='zlib')
...