hueseyincelik/holoaverage

Reconstruction and averaging of off-axis electron holograms as obtained by transmission electron microscopes.

About

Holoaverage is a Python program for the reconstruction and averaging of series of off-axis electron holograms recorded in a transmission electron microscope. The averaging is performed iteratively, such that instabilities of the microscope, like specimen and biprism drifts, can be tracked and corrected between consecutive exposures.

The program is written and maintained by Tore Niermann (email: [email protected]).

Details on the usage can be found in the documentation. The documentation can be found at

https://holoaverage.readthedocs.io

Citation

When you use the program in your research work, please cite the paper describing the details of the averaging method. The details can be found in

T. Niermann and M. Lehmann

Averaging scheme for atomic resolution off-axis electron holograms

Micron 63 (2014) 28-34

doi: 10.1016/j.micron.2014.01.008

The BibTeX entry for the paper is:

@article{Niermann2014,
    title = "Averaging scheme for atomic resolution off-axis electron holograms",
    journal = "Micron",
    volume = "63",
    pages = "28 - 34",
    year = "2014",
    doi = "https://doi.org/10.1016/j.micron.2014.01.008",
    author = "T. Niermann and M. Lehmann",
    keywords = "Off-axis electron holography, High-resolution transmission electron microscopy, Iterative reconstruction"
}

Installation

The program is a Python program. Thus, a working Python 3.X distribution is required for running it (support for Python 2.X has been dropped since version 1.1.8). Beside the Python interpreter it requires the following packages:

• numpy (see www.numpy.org)
• scipy (see www.scipy.org)
• h5py (see www.hypy.org)
• pyFFTW is optional; speeds up the averaging (see https://pypi.python.org/pypi/pyFFTW)

The package is tested with following Python versions:

• Python 3.6, numpy 1.11, scipy 0.19, h5py 2.7, PyFFTW 0.10
• Python 3.8, numpy 1.23, scipy 1.9, h5py 3.7, PyFFTW 0.13

The package can be most conveniently installed using the pip package manager. Make sure you have Python installed and the Python interpreter is in your path. Go to the command line and execute:

python3 -m pip install --upgrade holoaverage

Holoaverage leverages the pyFFTW package for speed. If pyfftw can not be installed you can still use holoaverage without problems. You can install pyFFTW by

python3 -m pip install --upgrade pyfftw

Up to date source versions can be found on the GitHub site: https://github.com/niermann/holoaverage

Bug reporting

When reporting a bug please include:

• Your operating system name and version.
• Any details about your local setup that might be helpful in troubleshooting.
• Detailed steps to reproduce the bug.

License

Holoaverage, program for reconstruction and averaging of electron holograms
Copyright (C) 2018-2022 Tore Niermann

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.