1 files changed, 122 insertions, 0 deletions
diff --git a/doc/articles/electrons.rst b/doc/articles/electrons.rst
new file mode 100644
index 00000000..c1a7ab2c
--- /dev/null
+++ b/doc/articles/electrons.rst
@@ -0,0 +1,122 @@
+==================================================
+Processing electron diffraction data with CrystFEL
+==================================================
+
+Electron diffraction data is fully supported in recent versions of CrystFEL.
+For some background, see this paper:
+
+R. Bücker, P. Hogan-Lamarre, P. Mehrabi, E. C. Schulz et al. "Serial protein
+crystallography in an electron microscope". Nature Communications 11 (2020)
+996. `doi:10.1038/s41467-020-14793-0 <https://doi.org/10.1038/s41467-020-14793-0>`_
+
+Here are some tips to get you started with your own data.
+
+
+Setting the wavelength
+======================
+
+You can set the accelerating voltage in the geometry file::
+
+  electron_voltage 300 kV
+
+This should be the accelerating voltage, not the relativistically-corrected
+energy of the accelerated electrons (the difference is small).  Alternatively,
+give the wavelength directly::
+
+  wavelength 2.51e-12 m
+
+You can also use `V` instead of `kV` and `A` (Angstroms) instead of `m`.
+
+Obviously, do not use `photon_energy` - that's only for electromagnetic
+radiation.
+
+
+Lens distortions and variable direct beam position
+==================================================
+
+Depending on the method of data acquisition, the central beam may vary from
+frame to frame quite a lot.  These shifts will need to be determined and stored
+in the image headers as part of a pre-processing step such as that performed by
+`diffractem <https://github.com/robertbuecker/diffractem>`_.  Specify the
+location of the shifts in the geometry file, for example::
+
+  detector_shift_x = /%/shots/shift_x_mm mm
+  detector_shift_y = /%/shots/shift_y_mm mm
+
+The location (`/%/shots/shift_x_mm`) will, of course, depend on your
+pre-processing.  These are the correct locations for data from `diffractem`.
+
+Note that the coordinates are shifts of the *detector* (not the *beam*) in the
+*laboratory coordinate system* (see `man crystfel_geometry`).  Shifts in
+"detector coordinates" (i.e. `detector_shift_fs`) would only make sense for
+single-panel detectors and are therefore not implemented.
+
+Correcting elliptical distortions of the projector lens can be done quite well
+by setting the panel direction vectors (see `man crystfel_geometry` again) to be
+non-orthogonal.  For example::
+
+  p0/fs = +0.9934x -0.0092y
+  p0/ss = -0.0092x +1.0067y
+
+This is also covered by `diffractem`.
+
+
+Indexing patterns
+=================
+
+The only indexing method suitable for electrons is PinkIndexer, but more
+methods might be added in the future.  As well as selecting the indexing method
+using `--indexing=pinkindexer`, you will need to configure PinkIndexer's
+assumption about the size of a reflection in reciprocal space using
+`--pinkIndexer-reflection-radius=0.003`::
+
+  indexamajig -g sample.geom -i input-files.lst -o sample.stream \
+              --indexing=pinkindexer --pinkIndexer-reflection-radius=0.003 \
+              --peaks=zaef --threshold=300 --min-squared-gradient=50000
+
+That's it!  You will have to tune the peak search parameters as usual, of
+course, but this should already be enough to get started with electron
+diffraction data.
+
+The default parameters give quick and reasonably good indexing.  You can get
+more accurate results by increasing the granularity of refinement within
+Pinkindexer using `--pinkIndexer-refinement-type=N`, with `N` from 0 (least
+precise and fastest) to 5 (most precise and slowest).  The default value is 1.
+
+For speed, you might want to add `--max-indexer-threads=N`, where `N` is the
+number of threads that PinkIndexer should use within itself.  You should also
+use `-j M` to specify the number of frames that `indexamajig` should process in
+parallel.  The sum of `N` and `M` should be roughly the number of available CPU
+cores.  It's also useful to try indexing each pattern only once (`--no-retry`).
+
+If the camera length is specified in the geometry file by referencing values
+from image file headers, then you will also need to give an estimate of the
+camera length using `--camera-length-estimate`.  The same applies if the
+wavelength is specified indirectly, in which case you will need
+`--wavelength-estimate`.  Neither of these are usually necessary for electron
+diffraction data.
+
+
+Saving and re-loading indexing results
+======================================
+
+Indexing patterns with PinkIndexer can take a long time, which makes it painful
+to try (for example) different integration parameters.  To mitigate this, you
+can store the results from one run of `indexamajig` and re-run the process
+using the previous indexing results instead of repeating the PinkIndexer step.
+
+First, create a *solution file* from the stream using the `stream2sol.py`
+program from the CrystFEL scripts folder::
+
+  stream2sol.py -i sample.stream -o sample.sol
+
+Then, run `indexamajig` using `--indexing=file` and giving the filename::
+
+  indexamajig -g sample.geom -i input-files.lst -o output.stream \
+              --indexing=file --fromfile-input-file=sample.sol \
+              --no-refine --no-check-peaks --no-retry \
+              --int-radius=10,12,14
+
+Note the options `--no-refine --no-check-peaks --no-retry` are added to skip
+the checks and refinement stages normally performed after indexing - these are
+not necessary when replaying solutions like this.