examples/spisonet.md
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+## spIsoNet Misalignment Correction Example
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+
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+This example for Misalignment is largely drawn from [the original spIsoNet tutorial](https://github.com/IsoNet-cryoET/spIsoNet/commit/c31f4156669f8e34ade8ba019efc3ba2276e0158), using data described in [the manuscript](https://doi.org/10.1038/s41592-024-02505-1) hosted at [Zenodo](https://zenodo.org/records/12640059).
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+
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+### Downloading tutorial data
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+This tutorial data is ~20G compressed, and will need ~30-35G space available to run.
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+```
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+#!/usr/bin/env bash
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+
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+wget "https://zenodo.org/records/12640059/files/Misalignment_Correction_tutorial.tar.gz"
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+if [ ! -d tutorial/ ] ; then
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+ tar zxvf Misalignment_Correction_tutorial.tar.gz
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+else
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+ echo "tutorial directory already present, not unpacking"
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+fi
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+
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+```
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+
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+### Running the misalignment correction
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+
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+This will default to using all available GPUs, but the number of MPI processes may need to be adjusted appropriately.
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+It should be run within the tutorial directory unpacked above.
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+
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+```
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+#!/usr/bin/env bash
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+source /programs/sbgrid.shrc
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+
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+export RELION_X=4.0.2_cu12.2
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+export RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE="relion_wrapper.py"
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+export CONDA_ENV="spisonet"
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+JOBDIR=job001
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+
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+if [ ! -d Refine3D/${JOBDIR} ] ; then
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+ mkdir -p Refine3D/${JOBDIR}
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+else
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+ echo "job directory already present"
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+ echo "please update the example, remove the existing directory, or run in a different location"
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+ echo "bailing out now"
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+ exit 1
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+fi
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+
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+mpirun.relion -np 3 `which relion_refine_mpi` --o Refine3D/${JOBDIR}/run --auto_refine --split_random_halves --i job025_tutorial.star --ref HA_reference.mrc --firstiter_cc --ini_high 10 --dont_combine_weights_via_disc --pool 30 --pad 2 --ctf --particle_diameter 170 --flatten_solvent --zero_mask --solvent_mask mask.mrc --solvent_correct_fsc --oversampling 1 --healpix_order 2 --auto_local_healpix_order 5 --offset_range 5 --offset_step 2 --sym C3 --low_resol_join_halves 40 --norm --scale --j 4 --gpu "" --external_reconstruct --keep_lowres --pipeline_control Refine3D/${JOBDIR}/
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+
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+```