Our lab's software contributions:

Updated review on serial crystallography data analysis coming soon to a special edition of Crystals https://www.mdpi.com/journal/crystals

Software

DatView - software for exploring very large serial crystallography datasets & much more. Download link, tutorial, manual, example data etc, available via https://zatsepinlab.atlassian.net/wiki/spaces/DAT/overview

Download DatView from here & please cite if used for your publications.

SPIND - software for auto-indexing sparse patterns in serial 'snapshot' crystallography. https://zatsepinlab.atlassian.net/wiki/spaces/SPIN/overview and https://github.com/LiuLab-CSRC/SPIND

Read about SPIND here: Chufeng Li et al. 2019 IUCrJ 6(), 72-84.

CrystFEL - software suite for serial crystallography with an an FEL (or synchrotron or any serial crystallography), the development of which is led by Thomas White at CFEL, DESY. It is the first and most cited serial crystallography data analysis software.

CrystFEL calls indexing modules for high-throughput autoindexing. It can currently index with MOSFLM, DirAx, XDS, felix, TakeTwo, SPIND (Chufeng's sparse indexer, currently interfaced with CrystFEL only through the version of SPIND on the SPIND github page), asdf (CrystFEL's internal algorithm) and since CrystFEL 0.8.0, it also interfaces with a recently added powerful algorithm, Xgandalf,

No programming expertise needed; very well documented & supported; under constant development. It has been used for almost a decade of XFEL serial femtosecond crystallography and serial millisecond crystallography at synchrotron sources.

BioXFEL STC related

• BioXFEL beamtime archive - All XFEL and synchrotron serial crystallography beamtimes from 2009 until now. BioXFEL collaborations only, since 2013. (Public version of archive seems to have moved but might be searchable on www.bioxfel.org)
• BioXFEL resources page
• LCLS data analysis - detailed instructions for LCLS (2016).
• ASU BioXFEL beamtime and data management - not updated since 2018.
• BioXFEL data analysis group resources - Scripts, tutorials, documentation for serial femtosecond crystallography analysis. You’ll need to sign in to bioxfel.org, which is quick & free.

Workshops

While part of BioXFEL, I ran multiple serial femtosecond crystallography workshops in the US (approximately annually), starting with an expert-filled two-day workshop held at Berkeley lab in 2014, then a few at ACA annual meetings. In 2019 we ran a mini-workshop in sample delivery options for protein microcrystals (primarily) as part of the BioXFEL 6th annual conference, which I cochaired with Prof. Brenda Hogue (ASU). Click link to learn more.

Future workshops will be held in Australia in 2021 onwards. Watch this space or email me for updated info: n.zatsepin at latrobe edu au

Other serial crystallography data analysis and related resources

Serial femtosecond crystallography software

ccpxfel - https://aip.scitation.org/doi/10.1063/1.4961470 - can only index with TakeTwo or the indexing tool from DIALS. Developer: Helen Ginn.

cctbx.xfel - need to know some python. Nick Sauter, Aaron Brewster et al.

nXDS - described here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118830/ and demonstrated on synchrotron serial crystallography in Kovacsova et al. (2017). Viscous hydrophilic injection matrices for serial crystallography. IUCrJ (2017). M4, 400-410 . Wolfgang Kabsch, Kay Diederichs.

This special issue of J. Appl. Cryst (http://journals.iucr.org/special_issues/2016/ccpfel/) has some extra tools that will be handy. As far as I know, all tools designed for XFEL serial crystallography should work for serial synchrotron data too, so don't ignore papers with the "XFEL" clickbait titles. They just get published more rapidly :)

Radiation damage

https://freedam.desy.de/

Olof Jönsson et al. (2018) High. Ener. Dens. Phys. and Scott, H. A. (2001) J. Quant. Spectrosc. Radiat. Transf. 71:689

FreeDam (Free Electron Laser Damage Simulation Database) is an online resource for damage simulations of various materials when exposed to an intense X-ray free electron laser pulse. The simulations are made with a non-LTE plasma software.

Linac Coherent Light Source data analysis using psana

D. Damiani, M. Dubrovin, I. Gaponenko, W. Kroeger, T. J. Lane, A. Mitra, C. P. O’Grady, A. Salnikov, A. Sanchez-Gonzalez, D. Schneider and C. H. Yoon J. Appl. Cryst. (2016). 49, 672-679 doi:10.1107/S1600576716004349

OnDA

OnDA development is led by Valerio Mariani at CFEL, DESY

Online Data Analysis and Feedback for Serial X-Ray Imaging

CSPAD Mask Maker

Written by Andrew Morgan at CFEL, DESY.

Very handy tool for making masks for the CSPAD.

Cheetah

Cheetah development is led by Anton Barty CFEL, DESY.

Cheetah is a set of programs for processing serial diffraction data data from at free electron laser sources, and which enable taking home only the data with meaningful content.

A. Barty, R. A. Kirian, F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White, and H. N. Chapman, “Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data,” J Appl Crystallogr, vol. 47, pp. 1118–1131 (2014). Article on IUCr website

CXIDB

Coherent X-ray Imaging Data Bank - archival for experimental data (lots from XFELs). Recent submissions include scripts for reproducing published results.

Computational Crystallography Newsletter