diffractem

Pre-processing software for serial electron diffraction (SerialED) data. See https://doi.org/10.1101/682575 for example results.

Diffractem is intended for usage within Jupyter notebooks - get a set of examples here: https://github.com/robertbuecker/serialed-examples.

Installation

diffractem is tailored to pre-processing SerialED data primarily for crystallographic analysis using CrystFEL, version 0.10.0 or higher: https://www.desy.de/~twhite/crystfel/index.html. To make most of diffractem's functionality, if you do not have it already, please download and install CrystFEL following the installation instructions given on its homepage. During the build process of CrystFEL using meson, the pinkIndexer component will automatically be downloaded and installed.

Create conda enivronment

We strongly suggest to use the Anaconda3 Python distribution/package manager, and create a dedicated environment within it for diffractem. If you do not have Anaconda installed, it is sufficient to obtain the minimal Miniconda of the conda package manager at https://docs.conda.io/en/latest/miniconda.

Once installed, please create a new anaconda environment for diffractem, and activate it:

conda create -n diffractem -c conda-forge python=3.10 numpy scipy pandas dask distributed jupyterlab ipywidgets ipympl tifffile h5py
conda activate diffractem

Install diffractem

Finally install diffractem itself, either from PyPi:

pip install diffractem

or, if you want to play/develop a bit more and stay up-to-date, you can clone this git repository and install diffractem in developer mode:

git clone https://github.com/robertbuecker/diffractem
cd diffractem
pip install -e .

Now you should be ready to go! To get started, why don't you download the example notebooks:

git clone https://github.com/robertbuecker/serialed-examples

And get example raw data at MPDL Edmond: https://edmond.mpdl.mpg.de/imeji/collection/32lI6YJ7DZaF5L_K.

And when you're ready to go: just make your own branches of the notebooks for your own projects, and have fun!

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diffractem, (C) 2019-2022 Robert Bücker, robert.buecker@rigaku.com

peakfinder8, (C) 2014-2019 Deutsches Elektronen-Synchrotron DESY