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 TBR
- CorrectCoordinates - correct the coordinates too near to the border of the imageTBR
- CreateMaskFromMap - using a binarized, thresholded mapTBR
- RunKerdenSOM - apply kerdensom to a set of 2D images or to a set of rotational power spectraTBR
- SubmitMpiJobOnJumilla - run parallel jobs using our Alpha queues.TBR
- ConvertXmdfileToRelionPosFile - After a classfication in Xmipp3, generate Pos file to extract particles in RelionTBR

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

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

- WebToXmippMark - How to convert coordinates of particles picked with Web (Spider) into a set of particles picked with XmippTBR
- 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 CTFTBR
- RunMpiProgramsWithoutRepeatingThePassword - How to run MPI programs without having to repeat the password for each process (depends on the UNIX distribution)TBR
- 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 XmippTBR
- RemoveOpenMPIWarnings - Remove OpenMPI warning about openib and udaplTBR
- EulerAngles - What is the interpretation of Euler angles in Xmipp
- HexDumpF - Hexdump of float numbers considering endiannessTBR
- ConvertingFrealignXmipp - Conversion of Euler angles from FRealign to XmippTBR
- ConvertingLstXmipp - Conversion of Eman lst files to XmippTBR
- DefinedMacros - How to know the macros defined by a compiler in a given systemTBR
- ConvertDownsamplePos - Convert and downsample posfiles of Xmipp 3.0 to Xmipp 2.4TBR
- ImportPosFromEmanAndSpider - Import coordinates from Eman and Spider into Xmipp 3.0TBR
- ApplyGeoInReconstructionMetadata - Given a metadata for reconstruction, generate the aligned images needed for reconstructing without shifts and mirrorsTBR
- GenerateTiltPairs - Generate untilted and tilted images for a given volumeTBR

- ConvertNewCTFModelOldCTF: convert from new ctf to oldTBR

- 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)TBR
- ScaleShifts - to reuse angles and shifts found in the previous projection matching runTBR

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