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pyaf

pyAF is a tool to analyze force curves & maps acquired by atomic force microscopes

https://github.com/sebastienjanel/pyaf

Science Score: 39.0%

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Repository

pyAF is a tool to analyze force curves & maps acquired by atomic force microscopes

Basic Info
  • Host: GitHub
  • Owner: sebastienjanel
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage: https://cmpi.cnrs.fr
  • Size: 1.03 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License Authors Codemeta

README.md

pyAF : An AFM Force Curve Analysis Software

pyAF is a Python software to analyze force curves & force maps acquired by atomic force microscopes (Bruker and JPK). Developed at CMPI lab (https://cmpi.cnrs.fr).

It computes: - Elasticity with several models and bottom effect correction (BEC) - Stiffness tomography - Work of detachment and rupture force - Unbinding events and loading rates - Zero-force topography - Regions of interest for substrate definition and stats - Curve tilt correction and smoothing - 3D map rendering - Text export (to R), Statistics (UNPOLISHED) - Multi files and (partial) multiprocessing

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".

Main coding made by Michka Popoff (https://theses.fr/api/v1/document/2014LIL10220). Modified by Antoine Dujardin, Simone Bovio, Javier Lopez-Alonso, Nuno Duarte, Sébastien Janel.

When using the program, cite the original article : Stiffness tomography of eukaryotic intracellular compartments by atomic force microscopy (Nanoscale, 2019,11, 10320-10328). DOI https://doi.org/10.1039/C8NR08955H

DISCLAIMER: pyAF is a lab-developed software, it is not a commercial software. Check as much as possible results provided vs other software (e.g. JPK DP) to rule out any no supported edge cases!

INSTALL procedure with PyCharm software (free for academics): - clone the repository (https://github.com/sebastienjanel/pyAF.git) in PyCharm (File/Project from Version Control) - install/select a Python3 interpreter - install required packages from the terminal of PyCharm: pip install -r requirements.txt - configure the Run/Debug configuration by choosing the script /pyAF/main.py with the Python version of your venv - click run - report bugs!

Owner

  • Login: sebastienjanel
  • Kind: user

CodeMeta (codemeta.json) 

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  "dateCreated": "2014-12-01",
  "dateModified": "2025-01-20",
  "datePublished": "2025-01-20",
  "description": "pyAF is a Python software to analyze force curves & force maps acquired by atomic force microscopes (Bruker and JPK)",
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  "referencePublication": "https://doi.org/10.1039/C8NR08955H"
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Dependencies

package-lock.json npm
requirements.txt pypi
  • PyQt5 ==5.15.11
  • QtPy ==2.4.3
  • h5py ==3.13.0
  • itk ==5.4.0
  • lmfit ==1.3.3
  • matplotlib ==3.10.1
  • numpy ==2.2.4
  • packaging ==24.2
  • pandas ==2.2.3
  • pillow ==11.1.0
  • psutil ==7.0.0
  • qtwidgets ==1.1
  • scipy ==1.15.2
  • seaborn ==0.13.2
  • setuptools ==78.0.2
  • tables ==3.10.2
  • vtk ==9.4.1
setup.py pypi
  • py2app *