This a list of commonly used scripts for processing of electron microscopy images. Please feel free to share your own.

- BoxerToXmippMark - translate the coordinates of EMAN's Boxer to Xmipp_Mark
- CorrectCoordinates - correct the coordinates too near to the border of the image
- CreateMaskFromMap - using a binarized, thresholded map
- RunKerdenSOM - apply kerdensom to a set of 2D images or to a set of rotational power spectra
- SubmitMpiJobOnJumilla - run parallel jobs using our Alpha queues.
- ConvertXmdfileToRelionPosFile - After a classfication in Xmipp3, generate Pos file to extract particles in Relion

- FromXmippToVariance3D - use Pawel Penzeck's Spider scripts after an Xmipp alignment
- SelectionFileSpidertoXmipp - convert Spider selection file (with numbers only) to an Xmipp selfile
- XmippPreprocessing - Tiff2raw, CTF-estimation, extraction, normalization, phase correction etc.
- MovingParticles - analyze the behaviour of your particles in a ML classification experiment.
- SortImagesBasedOnDocfile - Make a sorted selfile from a newxmipp style docfile (e.g. sort by CC).
- CtffindToXmippCtfParam - convert the .ctf file from CTFFIND to an XMIPP CTF-parameter file
- CompareClassAveragesWithReprojections - Align reference-free class averages with projections of a 3D model and visualize

- OpenDX - visualize Xmipp volumes in opendx
- CompareVolumeT using python (Note volumeT is the base clase of VolumeXmipp)
- xmipp_trimalifile.py.txt: - Extract a subaligned file from an aligned series using trimvol
- virus_symmetry_partners.py.txt: produce set of symmetry related volumes
- virus_extract_vertex.py.txt: extract vertex from a icosahedral virus
- CTFParamOldNew Convert ctf from old to new (metadata
- Convert xmipp 3 .pos files to xmipp 2.4 pos files
- Convert ctffind3 data to xmipp

- WebToXmippMark - How to convert coordinates of particles picked with Web (Spider) into a set of particles picked with Xmipp
- EstimatingNoisePowerForAGivenSNR - How to estimate how much noise to add to a set of phantom projections to have a given average SNR
- CoSSSmallTricks - How to generate an empty image, compute a radial average, ...
- EstimateTheCTF - How to estimate the CTF
- RunMpiProgramsWithoutRepeatingThePassword - How to run MPI programs without having to repeat the password for each process (depends on the UNIX distribution)
- CorrectingMisalignmentOfPDB - How to look for a misaligned rotational symmetry axis in a PDB and correct it
- HowManyReferenceProjections - What is the number of reference projections given an angular step
- EquivalentEulerAngles - Given an Euler angle, what are the Euler angles of its X, Y and XY mirrors and how are they expressed with another set of angles
- ConvertImagesToXmipp - Given images in EMAN, CCP4, Spider, ... How to convert them to Xmipp
- RemoveOpenMPIWarnings - Remove OpenMPI warning about openib and udapl
- EulerAngles - What is the interpretation of Euler angles in Xmipp
- HexDumpF - Hexdump of float numbers considering endianness
- ConvertingFrealignXmipp - Conversion of Euler angles from FRealign to Xmipp
- ConvertingLstXmipp - Conversion of Eman lst files to Xmipp
- DefinedMacros - How to know the macros defined by a compiler in a given system
- ConvertDownsamplePos - Convert and downsample posfiles of Xmipp 3.0 to Xmipp 2.4
- ImportPosFromEmanAndSpider - Import coordinates from Eman and Spider into Xmipp 3.0
- ApplyGeoInReconstructionMetadata - Given a metadata for reconstruction, generate the aligned images needed for reconstructing without shifts and mirrors
- GenerateTiltPairs - Generate untilted and tilted images for a given volume

- ConvertNewCTFModelOldCTF: convert from new ctf to old

- If you have performed a projection matching after downsampling the micrographs by a certain factor, and now want to proceed with a different downsampling factor (eg to use a finer pixel size), you may find the next two shell scripts useful:
- ScalePos - to write new .pos files according to the new downsampling (so you do not have to pick particles again)
- ScaleShifts - to reuse angles and shifts found in the previous projection matching run

- ReName: recursively rename micrographs and related files so they are prefixed with a number and postfixed with resolution.