TIMEleSS Multigrain Wiki

geometry

smerkel (smerkel@undisclosed.example.com) — 2026-08-12T03:35:58+00:00

Multigrain crystallography experiment geometry Experiment geometry Geometry and axes are important for multigrain crystallography experiment. You need to know how is your experiment relative, how are you rotating, what are x, y, z axes ? The figure below gives an outline of a typical definition of laboratory axes and angles

search_for_peaks

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:55:38+00:00

Search for peaks Once your processed your images, removed your background, etc, you are ready to extract peaks. Searching for diffraction spots in usually performed using peaksearch. To do so, you should look at some random peaks from several images by zooming in (in the

clean-diamond-anvil-cell-data

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:51:53+00:00

Clean up diamond anvil cell data Typical diamond anvil cell data for multigrain XRD has to be pre-processed and cleaned. Elements that should be addressed are: * shadows from the tungsten carbide diamond seats, * single-crystal diffraction spots from the diamond anvils,

backgrounddac

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:49:09+00:00

Evaluate background One necessary step of the data processing is the subtraction of the background. One way to do it is to create an average or a median image of the whole file series and then subtract each single image by this average/median. This method has the advantage that you not only get rid of the background noise but also all those reflections which are visible homogeneously in every image, such as pressure media, artefacts on the detector or some diamond spots.

timeless_viewer

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:47:01+00:00

TIMEleSS Viewer The TIMEleSS viewer is a simple application to view series of 3D-XRD data files. It is built on top of silx which was developed at ESRF to provide a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. silx aims to provide reading/writing tools for different file formats, data reduction routines and a set of Qt widgets to browse and visualise data.

backgroundgeneral

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:45:12+00:00

Background evaluation and subtraction Diffraction data typically include multiple contributions. These include * noise, from the detector, the source, etc * diffraction from anything within the path of the x-ray beam, which is not your sample,

convertfileseries

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:37:48+00:00

Convert image file series Introduction Typical diamond anvil cell beamlines generate series of diffraction files in various formats, which are not the EDF format used in further processing. The tools here can be used to convert the files into the proper format.

grainspotter

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:28:47+00:00

GrainSpotter GrainSpotter is a software which looks for grains in a 2D diffraction image. It was developed by S. Schmidt, Technical University of Denmark. See the publication for more information: Søren Schmidt GrainSpotter: a fast and robust polycrystalline indexing algorithm

minimal_software_intallation

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T08:22:22+00:00

Getting started with a Python environment There is a whole suite of software required to run multigrain X-ray diffraction, and their installation procedure can be quite tricky if you are not comfortable with computing techniques. The recommended method is to install a python dedicated environement. This has been tested on Linux, but should also work on mac and windows, if you have a working python installation (

gettingstartedmax

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T07:05:00+00:00

Getting started with Anaconda A minimal set of data processing tools could include * TIMEleSS Viewer : to look at diffraction images and median calculations * ImageD11: script for peak search, experimental parameters refinement, peak assignment, can do grain indexing, and many others

sidebar

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T06:53:19+00:00

Introduction * About this wiki * Literature Software * General * Introduction * Getting started with Anaconda * Getting started with a python environement (recommended) * Individual packages * TIMEleSS Viewer * Peaksearch * ImageD11 * GrainSpotter * PolyXSim * FitAllB * xfab * TIMEleSS tools * MTeX * VESTA Experiment * Experiment geometry * Sample preparation Pre-processing X-Ray Data * Convert file series to EDF Data processing * …

timeless_viewer_mainwindow.png - created

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T06:46:06+00:00

start - [Minimal installation]

smerkel (smerkel@undisclosed.example.com) — 2026-08-10T06:35:43+00:00

Multigrain data processing software We rely heavily on software written for the fable project. Fable is a collection of packages for multigrain crystallography. Some are still maintained, others have not been touched for 10 years. Recently, a new website was started:

gay2023_bridgmanite_2dplot.png - created

smerkel (smerkel@undisclosed.example.com) — 2023-12-10T08:02:07+00:00

illuminated_volume_new.png - created

matthias (matthias@undisclosed.example.com) — 2021-04-21T08:48:28+00:00

histogram-example.jpg - created

matthias (matthias@undisclosed.example.com) — 2021-04-20T11:49:01+00:00

histogram-test-maud.png - created

smerkel (smerkel@undisclosed.example.com) — 2021-02-10T11:55:42+00:00

2theta-histogram.png - created

smerkel (smerkel@undisclosed.example.com) — 2021-02-10T11:33:12+00:00

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matthias (matthias@undisclosed.example.com) — 2020-10-06T15:09:52+00:00

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matthias (matthias@undisclosed.example.com) — 2020-10-06T15:09:33+00:00

qz2mgc2_st_43gr_ipf_hw15.jpg - created

matthias (matthias@undisclosed.example.com) — 2020-10-06T13:47:21+00:00

qz2mgc2_st_43gr_ipf_hw10.jpg - created

matthias (matthias@undisclosed.example.com) — 2020-10-06T13:46:32+00:00

general_data_processing_flow_chart_.png

matthias (matthias@undisclosed.example.com) — 2020-03-25T09:35:38+00:00

vesta.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-12-05T09:52:32+00:00

ipf-grains-indexing-1.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-12-04T11:46:45+00:00

grains-indexing-1.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-12-04T11:45:25+00:00

indexations-1-2-3.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-12-03T14:50:35+00:00

diamond-removed-inpaint.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-09-03T13:54:11+00:00

diamond-removed-median-peaks.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-09-03T13:54:00+00:00

diamond-removed-median.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-09-03T13:53:50+00:00

orginal-image.jpg - created

smerkel (smerkel@undisclosed.example.com) — 2019-09-03T13:53:34+00:00