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 CrystFEL - Data processing for serial crystallography
 =====================================================
 
-Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY,
-                      a research centre of the Helmholtz Association.
+Overview
+--------
 
-See AUTHORS as well as individual source code files for full details of contributors.
+CrystFEL is a suite of programs for processing data from [serial
+crystallography experiments](https://en.wikipedia.org/wiki/Serial_Femtosecond_Crystallography),
+performed at synchrotron and X-ray free-electron laser facilities, as well as
+in your home lab using an electron microscope.
 
-Introduction
-------------
 
-CrystFEL is a suite of programs for processing (and simulating) Bragg
-diffraction data from "serial crystallography" experiments, often (but not
-always) performed using an X-ray Free-Electron Laser.  Compared to rotation data,
-some of the particular characteristics of such data which call for a
-specialised software suite are:
+Getting started
+---------------
+
+See [INSTALL.md](INSTALL.md) for installation instructions, including
+installation via package manager and details of pre-existing installations at
+X-ray facilities around the world.
+
+CrystFEL can be used from the command line or via a graphical user interface.
+To start the graphical user interface, run ```crystfel```.
+
+There is a [video tutorial](https://vimeo.com/585412404), as well as a [text
+tutorial](doc/articles/tutorial.rst) to get you started with processing via the
+GUI.
+
+For command-line use, standard ```man``` pages are available.  Start with
+```man crystfel```.  The manual pages are also
+[available on the web](https://www.desy.de/~twhite/crystfel/manual.html).
+
+
+Documentation
+-------------
+
+* [Basic Tutorial](doc/articles/tutorial.rst)
+* [How to choose the right point group for merging](doc/articles/pointgroup.rst)
+* [How to increase data processing speed](doc/articles/speed.rst)
+* [Real-time data processing](doc/articles/online.rst)
+* [Processing electron diffraction data](doc/articles/electrons.rst)
+* [Symmetry classification for serial crystallography](doc/twin-calculator.pdf)
+* [Matrix conventions used in CrystFEL code](doc/matrix-notation.pdf) - for
+  developers, written mostly for my own benefit.
+* [Hit rate graph](doc/hitrate.png)
+* [Examples folder](doc/examples) - contains some template input files.
+* [Contributing to CrystFEL](CONTRIBUTING.md) - including how to cite CrystFEL
+  and how to find good first issues to work on.
+* [Citation list](https://www.desy.de/~twhite/crystfel/citations.html) - please
+  send us details of your paper, if it's missing!
+* [Scripts folder](scripts) - a miscellany of smaller programs to help at
+  various stages of data processing.
+
+
+Journal articles and book chapters
+----------------------------------
+
+* [Processing serial crystallography data with CrystFEL: a step-by-step
+  guide](https://doi.org/10.1107/S205979831801238X) - covers command-line
+  processing only (pre-dates the GUI).
+* [Recent developments in CrystFEL](http://dx.doi.org/10.1107/S1600576716004751) -
+  now somewhat out of date, but contains some useful information about the
+  algorithms used.
+* [Crystallography and Molecular Imaging using X-ray
+  Lasers](https://doi.org/10.23730/CYRSP-2018-001.605) - an introduction to the
+  biological aspects and possibilities, written for physicists (in contrast to
+  most other articles, which introduce the physical aspects for biologists!).
+* [Original paper about CrystFEL](http://dx.doi.org/10.1107/S0021889812002312)
+  from 2012.  Not open access, but a "reprint" is available
+  [here](https://www.desy.de/~twhite/crystfel/db5097-reprint.pdf).
+* [Climbing the Data Mountain: Processing of SFX
+  Data](https://link.springer.com/chapter/10.1007/978-3-030-00551-1_7) -
+  emphasizes data volume issues for XFELs.  Unfortunately not open access.
+* [Processing of XFEL
+  Data](https://link.springer.com/protocol/10.1007/978-1-4939-7000-1_13) -
+  describes the entire processing pipeline.  Unfortunately not open access.
+
+
+Awards
+------
+
+In 2017, the development of CrystFEL was recognised with the [Max von Laue
+Prize](https://www.desy.de/news/news_search/index_eng.html?openDirectAnchor=1202)
+from the [German Society for Crystallography (DGK)](https://dgk-home.de/en/).
 
-* The sliced, rather than integrated, measurement of intensity data.  Many, if
-  not all reflections are partially integrated.
 
-* Many patterns (thousands) are required - high throughput is needed.
+Funding acknowledgements
+------------------------
 
-* The crystal orientations in each pattern are random and uncorrelated.
+Development of CrystFEL is primarily funded by the
+[Helmholtz Association](https://www.helmholtz.de/) via
+[DESY](https://www.desy.de/).
 
-* Merging into lower symmetry point groups may require the resolution of
-  indexing ambiguities.
+Partial funding for CrystFEL has previously been provided by:
 
+* European Union’s Horizon 2020 research and innovation programme under grant
+  agreement No 857641 ([ExPaNDS](https://expands.eu/)) (2019-2023).
 
-Getting started
----------------
+* [X-Probe](http://x-probe.org/), a project of the European Union's 2020
+  Research and Innovation Program Under the Marie Skłodowska-Curie grant
+  agreement 637295 (2015-2018).
 
-See INSTALL.md for installation instructions.
+* The [BMBF](https://www.bmbf.de/) German-Russian Cooperation
+  [SyncFELMed](http://www.syncfelmed.org/), grant 05K14CHA (2014-2017).
 
-The best way to get started, after installation, is to run command ```crystfel```
-to start the graphical user interface.
+* [BioStruct-X](https://www.biostruct-x.eu/), a project funded by the Seventh
+  Framework Programme (FP7) of the European Commission (2011-2016).
 
 
 Licence
 -------
 
+Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY, a research centre
+of the Helmholtz Association.
+
+See [AUTHORS](AUTHORS) as well as individual source code files for full details
+of contributors.
+
 CrystFEL 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
@@ -51,21 +127,3 @@ You should have received a copy of the GNU General Public License along with
 CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
 
 
-Funding acknowledgements
-------------------------
-
-Development of CrystFEL is primarily funded by the Helmholtz Association.
-
-Partial funding for CrystFEL has previously been provided by:
-
-- European Union’s Horizon 2020 research and innovation programme under grant
-  agreement No 857641 (ExPaNDS) (2019-2023).
-
-- "X-Probe", a project of the European Union's 2020 Research and Innovation
-  Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018).
-
-- The BMBF German-Russian Cooperation "SyncFELMed", grant 05K14CHA (2014-2017).
-
-- BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the
-  European Commission (2011-2016).
-