vLFD - The virtual Laboratory for Fluorescence Dynamics

by Christoph Gohlke and Oliver Holub, Laboratory for Fluorescence Dynamics

vLFD is educational software under development to disseminate the knowledge of basic optical fluorescence spectroscopic concepts and applications by simulating real world instrumentation and molecular processes.

vLFD will not be released anytime soon. However, software and code developed as part of vLFD will be made available for download as they become useful on their own.

Fluorescence Lifetime Demo

The "Lifetime Demo" displays time and frequency domain fluorescence curves, as well as fluorescence lifetime phasors and apparent single lifetimes as a function of excitation frequency, donor and acceptor lifetime, FRET efficiency, the percentage of donors undergoing FRET, the percentage of donor emission in the acceptor channel, the percentage of directly excited acceptors, the background intensity, and the excitation pulse width. The parameters are interactively adjustable. This demo has been scripted using the vLFD fluorescence library and matplotlib. Download vLFD.

Molecular Mass Calculator

"Molecular Mass Calculator" calculates the molar mass (average and isotopic pure), the elemental analysis and the molecular mass distribution of a molecule given by its chemical formula. It performs simple stoichiometric calculations and estimation of the empirical formula from experimentally determined element fractions. Calculations are based on the isotopic composition of the elements. Mass deficiency due to chemical bonding is not taken into account. Download vLFD .


Windows XP	GNOME	MacOS X

Periodic Table of Elements

"Periodic Table of Elements" displays various properties of the chemical elements. Download vLFD .


Windows XP	GNOME	MacOS X

Color Palette Converter

"Color Palette Converter " reads, displays, and saves color palettes (aka color lookup tables, LUTs or CLUTs) of various formats: Binary RGB(A) and RRGGBB(AA), Windows RIFF, Windows Indexed Bitmap, The GIMP, PaintShop Pro, Spyglass Transform (HDF), Excel CSV, ICOL, MRIcro, ImageJ, Amira Mesh, MAP, Zeiss LSM510, and MedicView. Download vLFD.


Windows XP

Download

vLFD is in the early stages of development and will not be released in its final form anytime soon. The following archives contain software developed along with vLFD:

vLFD for Microsoft Windows XP (vLFD.zip; 18.04 MB; October 29, 2007; requires Pentium IV compatible CPU)
This archive contains the executables, not the source code, of the aforementioned applications and demos as well as a complete runtime environment. No installation is needed: just extract the archive into the 'Program Files' or 'Users Home' directory, which will create a vLFD subdirectory.
Source code for Windows, MacOS and Linux (not yet available; requires Python, Numpy, Matplotlib, and wxPython)

Copyright: You may freely redistribute these files as long as the content remains complete and unchanged.

Disclaimer: Because these programs are provided free of charge, there is no warranty for the programs, to the extent permitted by applicable law. The programs are provided "as is" without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of the programs is with you. Should the programs prove defective, you assume the cost of all necessary servicing, repair or correction.

Python Modules

Some Python modules are released under BSD license terms.

Acknowledgments

Python (www.python.org), a dynamic object-oriented programming language.
IPython (ipython.scipy.org), an enhanced interactive Python shell.
Numpy (numpy.scipy.org), a fundamental package needed for scientific computing with Python.
SciPy (www.scipy.org), open-source software for mathematics, science, and engineering.
Matplotlib (matplotlib.sourceforge.net), a Python 2D plotting library.
wxPython (www.wxpython.org), a cross-platform Python GUI toolkit with native look and feel.
PIL (www.pythonware.com/products/pil), the Python Imaging Library, adds image processing capabilities to Python.
VTK (www.vtk.org), the Visualization Toolkit, a software system for 3D graphics, image processing, and visualization.
Tango (tango.freedesktop.org) helps to create a consistent graphical user interface experience.