<i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments
Serial crystallography (SX) is a cutting-edge technique in structural biology, involving the systematic collection of X-ray diffraction data from numerous randomly oriented microcrystals. To extract comprehensive three-dimensional information about the studied system, SX utilises thousands of measur...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-02-01
|
| Series: | Crystals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4352/14/2/164 |
| _version_ | 1797298474231791616 |
|---|---|
| author | Yaroslav Gevorkov Marina Galchenkova Valerio Mariani Anton Barty Thomas A. White Henry N. Chapman Oleksandr Yefanov |
| author_facet | Yaroslav Gevorkov Marina Galchenkova Valerio Mariani Anton Barty Thomas A. White Henry N. Chapman Oleksandr Yefanov |
| author_sort | Yaroslav Gevorkov |
| collection | DOAJ |
| description | Serial crystallography (SX) is a cutting-edge technique in structural biology, involving the systematic collection of X-ray diffraction data from numerous randomly oriented microcrystals. To extract comprehensive three-dimensional information about the studied system, SX utilises thousands of measured diffraction patterns. As such, SX takes advantages of the properties of modern X-ray sources, including Free Electron Lasers (FELs) and third and fourth generation synchrotrons, as well as contemporary high-repetition-rate detectors. Efficient analysis of the extensive datasets generated during SX experiments demands fast and effective algorithms. The <i>FDIP</i> library offers meticulously optimised functions tailored for preprocessing data obtained in SX experiments. This encompasses tasks such as background subtraction, identification and masking of parasitic streaks, elimination of unwanted powder diffraction (e.g., from ice or salt crystals), and pinpointing useful Bragg peaks in each diffraction pattern. The library is equipped with a user-friendly graphical interface for facile parameter adjustment tailored to specific datasets. Compatible with popular SX processing software like OnDA, Cheetah, CrystFEL, and Merge3D, the <i>FDIP</i> library enhances the capabilities of these tools for streamlined and precise serial crystallography analyses. |
| first_indexed | 2024-03-07T22:36:25Z |
| format | Article |
| id | doaj.art-454c66b102d04065b6b252a7f1bd06fa |
| institution | Directory Open Access Journal |
| issn | 2073-4352 |
| language | English |
| last_indexed | 2024-03-07T22:36:25Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Crystals |
| spelling | doaj.art-454c66b102d04065b6b252a7f1bd06fa2024-02-23T15:13:15ZengMDPI AGCrystals2073-43522024-02-0114216410.3390/cryst14020164<i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography ExperimentsYaroslav Gevorkov0Marina Galchenkova1Valerio Mariani2Anton Barty3Thomas A. White4Henry N. Chapman5Oleksandr Yefanov6Institute of Vision Systems, Hamburg University of Technology, Harburger Schloßtraße 20, 21079 Hamburg, GermanyCenter for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, GermanyCenter for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, GermanyDeutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, GermanyDeutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, GermanyCenter for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, GermanyCenter for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, GermanySerial crystallography (SX) is a cutting-edge technique in structural biology, involving the systematic collection of X-ray diffraction data from numerous randomly oriented microcrystals. To extract comprehensive three-dimensional information about the studied system, SX utilises thousands of measured diffraction patterns. As such, SX takes advantages of the properties of modern X-ray sources, including Free Electron Lasers (FELs) and third and fourth generation synchrotrons, as well as contemporary high-repetition-rate detectors. Efficient analysis of the extensive datasets generated during SX experiments demands fast and effective algorithms. The <i>FDIP</i> library offers meticulously optimised functions tailored for preprocessing data obtained in SX experiments. This encompasses tasks such as background subtraction, identification and masking of parasitic streaks, elimination of unwanted powder diffraction (e.g., from ice or salt crystals), and pinpointing useful Bragg peaks in each diffraction pattern. The library is equipped with a user-friendly graphical interface for facile parameter adjustment tailored to specific datasets. Compatible with popular SX processing software like OnDA, Cheetah, CrystFEL, and Merge3D, the <i>FDIP</i> library enhances the capabilities of these tools for streamlined and precise serial crystallography analyses.https://www.mdpi.com/2073-4352/14/2/164serial crystallographymasking artefactspeak finding algorithmreal-time feedback |
| spellingShingle | Yaroslav Gevorkov Marina Galchenkova Valerio Mariani Anton Barty Thomas A. White Henry N. Chapman Oleksandr Yefanov <i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments Crystals serial crystallography masking artefacts peak finding algorithm real-time feedback |
| title | <i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments |
| title_full | <i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments |
| title_fullStr | <i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments |
| title_full_unstemmed | <i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments |
| title_short | <i>FDIP</i>—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments |
| title_sort | i fdip i a fast diffraction image processing library for x ray crystallography experiments |
| topic | serial crystallography masking artefacts peak finding algorithm real-time feedback |
| url | https://www.mdpi.com/2073-4352/14/2/164 |
| work_keys_str_mv | AT yaroslavgevorkov ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments AT marinagalchenkova ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments AT valeriomariani ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments AT antonbarty ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments AT thomasawhite ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments AT henrynchapman ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments AT oleksandryefanov ifdipiafastdiffractionimageprocessinglibraryforxraycrystallographyexperiments |