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Laboratory for Fluorescence Dynamics (LFD) file formats

Project description

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. For example:

  • SimFCS VPL, VPP, JRN, BIN, INT, CYL REF, BH, BHZ FBF, FBD, B64, I64, Z64, R64
  • GLOBALS LIF, ASCII
  • CCP4 MAP
  • Vaa3D RAW
  • Bio-Rad(r) PIC
  • Vista IFLI
  • FlimFast FLIF

For command line usage run python -m lfdfiles --help

Author:Christoph Gohlke
Organization:Laboratory for Fluorescence Dynamics. University of California, Irvine
License:3-clause BSD
Version:2019.7.2

Requirements

Revisions

2019.7.2
Require tifffile 2019.7.2. Remove some utility functions.
2019.5.22
Read and write Bio-Rad(tm) PIC files. Read and write Voxx MAP palette files. Rename SimfcsMap to Ccp4Map and SimfcsV3draw to Vaa3dRaw. Rename save functions.
2019.4.22
Fix setup requirements.
2019.1.24
Add plots for GlobalsLif, SimfcsV3draw, and VistaIfli. Support Python 3.7 and numpy 1.15. Move modules into lfdfiles package.
2018.5.21
Update SimfcsB64 to handle carpets and streams. Command line interface for plotting and converting to TIFF. Registry of LfdFile classes. Write image and metadata to TIFF. Read TIFF files.
2016.3.29
Write R64 files.
2016.3.14
Read and write Vaa3D RAW volume files.
2015.3.02
Initial support for plotting.
2015.2.19
Initial support for new FBD files containing headers.
2014.12.2
Read B64, R64, I64 and Z64 files (SimFCS version 4).
2014.10.10
Read SimFCS FIT files.
2014.4.8
Read and write CCP4 MAP volume files.
2013.8.10
Read second harmonics FlimBox data.

Notes

Lfdfiles is currently developed, built, and tested on Windows only.

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

The Microsoft Visual C++ Redistributable Packages are required on Windows.

Many of the LFD’s 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.

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. FLOP 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.

Project details


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