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PyFRAP: A Python based FRAP analysis tool box.

Fluorescence Recovery After Photobleaching (FRAP) is a common way to assess molecular diffusion. PyFRAP is a novel simulation-based analysis software that makes use of PDE simulations to analyze FRAP experiments in 3D geometries. It uses the first post-bleach image as initial condition, making assumptions about the underlying initial conditions obsolete. PyFRAP can fit different reaction-diffusion models to FRAP data, providing quantitative information about effective diffusion.

Features

PyFRAP comes with a full image analysis and simulation toolbox. In particular, PyFRAP can

  • Import FRAP datasets from timelapse experiments and analyze image data with various options such as
    • image filters
    • background substraction
    • illumination correction
  • Simulate the FRAP experiment with exact interpolated initial conditions
  • Fit simulated experiment to analyzed data and extract diffusion coefficient
  • Statistical analysis of fitting results
  • Hierarchical data structure making data exchange/sharing easy
  • Comprehensive GUI, making almost all PyFRAP tools available

Installation

PyFRAP can be installed in different ways. We provide installation scripts that allow an easy installation of PyFRAP in combination with Anaconda, including all necessary Python packages and external softwares. Installation instructions can be found here.

If you are familiar with Python and git, you can install PyFRAP via

git clone https://github.com/alexblaessle/PyFRAP

and:

python setup.py install --user

We highly recommend installing with the --user option, since PyFRAP needs to read/write data files in the installation folder. In some cases, this might lead to file permission issues. For a full installation documentation, have a look at the wiki.

Requirements

PyFRAP depends on

  • numpy>=1.8.2
  • matplotlib>=1.4.3
  • scipy>=0.13.3
  • scikit-image>=0.11.3
  • fipy>=3.1
  • PyQT4>4.10.4
  • vtk>=5.8.0
  • colorama>=0.2.5
  • wget>=3.2
  • gmsh (compiled with TetGen Algorithm) MUST BE Version 2.14.0!

Note that the installation described here installs all necessary packages.

Getting Started

Running the PyFRAP GUI

PyFRAP comes with a comprehensive GUI. It can easily be started by clicking on runPyFRAP.bat (Windows), runPyFRAP.command (OSX) or runPyFRAP.sh (Linux).

If you are using a terminal, cd to your PyFRAP directory and type

python pyfrp/PyFRAP.py

If you are already in a python session, you can simply run

import pyfrp
pyfrp.main()

Note that in the latter method PyFRAP's stdout might get redirected to the python shell you are executing it from.

Running PyFRAP from the command line

PyFRAP is a complete python package and can be imported via

	import pyfrp

Note that PyFRAP has three main submodules: pyfrp.modules, pyfrp.subclasses and pyfrp.gui. If you do not want to use any GUI elements, we recommend only importing the modules you need.

Using the PyFRAP GUI to analyze a FRAP experiment

Check out the PyFRAP wiki's First Steps Section.

API

PyFRAP is fully documented, allowing easy creation of scripts and extensions of the PyFRAP toolbox. The API of PyFRAP can be found here .

Documentation

To learn more about PyFRAP, check out the PyFRAP wiki