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| AC | Auto Correlation || |
| AC MS | Auto Correlation - Masked and normalized || |
| AC MSS | Self Correlation - Masked and normalized || |
| AC N | Auto Correlation - Normalized || |
| AC NS | Self Correlation - Normalized || |
| AC S | Self Correlation || |
| AD | Add images |
| AD F | Add two images with factors |
| AD R | Add two images with ratio |
| AD S | Add Series of images |
| AP CA | Alignment - Classification and Alignment |
| AP CM | Alignment - Classification and Alignment |
| AP I | Alignment - Initalize Rings File || |
| AP MS | Alignment - multi-reference, shift alignment || |
| AP RA | Alignment - Reference-free rotational alignment || |
| AP REF | Alignment - multi-reference, rotation & shift ||* |
| AP SA | Alignment - Shift || |
| AP SCC | Alignment - multi-reference, translation alignment || |
| AP SH | Alignment - multi-reference, exhaustive rotation & shift ||* |
| AP SR | Alignment - reference free, Shift & Rotation || |
| AR | Arithmetic operation |
| AR IF | Arithmetic operation - IF allowed |
| AR SCA | Arithmetic scaling of image |
| AS | Average images - find variance |
| AS AD | Average images - add to an existing average |
| AS F | Average images - find statistics & Q factor map || |
| AS R | Average images - find & save variance, better |
| AT IT | Automatic particle picking - intermediate program. |
| AT PK | Automatic particle picking - peak search |
| AT SA | Automatic particle picking - statistical parameters || |
| AT WN | Automatic particle selection |
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| BC | Box Convolution |
| BL | Create Blank image |
| BP 32F | Back Projection - 3D, Odd-even, interpolated in Fourier space ||* |
| BP 3D | Back Projection - 3D, using Euler angles || |
| BP 3F | Back Projection - 3D, interpolated, in Fourier space ||* |
| BP CG | Back Projection - 3D, conjugate gradients, ||* |
| BP R2 | Back Projection - 2D, weighting of image series || |
| BP RP | Back Projection - 3D, iterative, with constraints, ||* |
| BP S2 | Back Projection - 2D, single tilt iterative, constrained || |
| BP W2 | Back Projection - 2D, filtered, weighted || |
| BPD 32F | Back Projection - 3D, Sampled, Interpolated in Fourier space ||* |
| BPD 3F | Back Projection - 3D, Interpolated in Fourier space ||* |
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| CA S | Correspondence Analysis - Solution |
| CA SM | Correspondence Analysis - Show Map & Eigen Values |
| CA SMI | Correspondence Analysis - Set Active/Inactive Images Coordinates |
| CA SR | Correspondence Analysis - Reconstitute images |
| CA SRA | Correspondence Analysis - Arbitrary image reconstitution |
| CA SRD | Correspondence Analysis - Reconstitute Differential images |
| CA SRE | Correspondence Analysis - Reconstitution of eigenimages |
| CA SRI | Correspondence Analysis - Reconstitute Importance images |
| CA VIS | Correspondence Analysis - Create Visual map |
| CC | Cross Correlation || |
| CC C | Cross Correlation Coefficient |
| CC MS | Cross Correlation - Masked and normalized || |
| CC N | Cross Correlation - Normalized || |
| CC P | Cross Correlation - Polar || |
| CE AD | Contrast Enhancement - Anisotropic Diffusion |
| CE FIT | Contrast Enhancement - FIT the histogram |
| CE FREI | Contrast Enhancement - Frei & Chen |
| CE G | Contrast Enhancement - Gradient |
| CE GNC | Contrast Enhancement - Graduated Non Convex restoration |
| CE HARALICK | Contrast Enhancement - Haralick |
| CE HI | Contrast Enhancement - Histogram Equalization |
| CE HURST | Contrast Enhancement - Hurst |
| CE LAH | Contrast Enhancement - Local Area Histogram |
| CE LAP | Contrast Enhancement - Laplacian |
| CE MAX | Contrast Enhancement - Maximum |
| CE MED | Contrast Enhancement - Median Filtering |
| CE MET | Contrast Enhancement - Maximum Entropy Threshold |
| CE MIN | Contrast Enhancement - Minimum |
| CE OD | Contrast Enhancement - adjust Optical Densities |
| CE OR | Contrast Enhancement - Local Orientation |
| CE PREWITT | Contrast Enhancement - Prewitt |
| CE RAN | Contrast Enhancement - Range |
| CE RIDGE | Contrast Enhancement - Ridge Following |
| CE SOBEL | Contrast Enhancement - Sobel |
| CE ST | Contrast Enhancement - Stretching |
| CE TOP | Contrast Enhancement - Top Hat |
| CE VAR | Contrast Enhancement - Variance |
| CE VS | Contrast Enhancement - Variance smoothing |
| CE WATER | Contrast Enhancement - Watershed Segmentation |
| CG | Center of Gravity |
| CG 3 | Center of Gravity - Radius of gyration |
| CG 3S | Center of Gravity - Solid body option |
| CG PH | Center of Gravity - Phase approximation || |
| CI | Confidence Interval |
| CL CLA | Classification - Clustering |
| CL HC | Classification - Hierarchical Clustering |
| CL HD | Classification - Hierarchical clustering, calculate classes |
| CL HE | Classification - Hierarchical clustering, create docfiles |
| CL KM | Classification - K Means clustering || |
| CN | Convolution || |
| CN N | Convolution - Normalized || |
| CO | Contour into Postscript file |
| CP | Copy SPIDER file to SPIDER file |
| CP FROM ASCII | Copy ASCII text file to SPIDER file |
| CP FROM CCP4 | Copy CCP4 format File to SPIDER file |
| CP FROM EMI | Copy EMISPEC format file to SPIDER file |
| CP FROM MRC | Copy MRC format file to SPIDER file |
| CP FROM NIKON | Copy Nikon Coolscan format file to SPIDER file |
| CP FROM PDB | Copy PDB file to SPIDER format |
| CP FROM PE | Copy Perkin Elmer disk file to SPIDER format |
| CP FROM RAW | Copy Raw Image to SPIDER file |
| CP FROM TERM | Copy Terminal input to SPIDER file |
| CP FROM VAX | Copy VAX SPIDER file to a Unix SPIDER file |
| CP FROM XP | Copy X-PLOR ASCII file to SPIDER file |
| CP I | Copy SPIDER file to Indexed SPIDER stack |
| CP TO ASCII | Copy SPIDER file to ASCII text format |
| CP TO BRIX | Copy SPIDER volume to BRIX file for "O" input |
| CP TO CCP4 | Copy SPIDER file TO CCP4 format file |
| CP TO MRC | Copy SPIDER file TO MRC format file |
| CP TO OPEND | Copy SPIDER file TO Opposite Endedness |
| CP TO POST | Copy SPIDER image to a POSTscript image |
| CP TO RAW | Copy SPIDER file to a 8-bit raw image |
| CP TO SGI | Copy SPIDER file to SGI format |
| CP TO TIFF | Copy SPIDER file to a TIFF format |
| CP TO VV | Copy SPIDER volume to Voxel View format |
| CP TO XPLOR | Copy SPIDER volume to X-PLOR format |
| CV REPL | Projection onto Convex sets - Replace projector |
| CYCLE | Starts next loop iteration |
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| FC | File Contouring |
| FC E | File Contouring - External contour levels |
| FD | Filter according to a Document file || |
| FF | Fourier Filter |
| FF PLOT | Fourier Filter - design filter |
| FI | File Information - place header value(s) in register variable |
| FI A | File Information - Multiple files |
| FI N | File Information - Do not halt if file not found |
| FI X | File Information - place header values in registers |
| FP | Fourier interpolation || |
| FQ | Filter - Quick Fourier, High, low pass, etc. || |
| FQ NP | Filter - Quick Fourier, High, low pass, etc, No Padding || |
| FR | Read (sets) a local symbolic parameter (string variable) |
| FR F | Read (sets) global symbolic parameter (string variable) from a file |
| FR G | Read (sets) a global symbolic parameter (string variable) |
| FR L | Read (sets) a local symbolic parameter (string variable) |
| FR N | Read (sets) next global symbolic parameter (string variable) from file |
| FS | Find Statistics |
| FS M | Find Statistics - within Mask |
| FT | Fourier Transform || |
| FT R | Fourier Transform Replace |
| FV | Find threshold for Volume |
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| HD | Histogram of Document file column - output in Results file |
| HD D | Histogram of Document file column - output in Document file. |
| HD R | Histogram of Document file column - output in Results file, use specified range |
| HF | Helical Fourier |
| HI | Histogram - output in Results file |
| HI D | Histogram - output in Document file |
| HI DR | Histogram - output in Document file, use specified Range |
| HI E | Histogram - to determine entropy |
| HI JOINT | Histogram - Joint, to determine mutual shared information |
| HI M | Histogram - within Masked area |
| HI R | HIstogram - output in Results file, use specified range. |
| HI T | Histogram - output on Terminal |
| HI TR | Histogram - output on Terminal, use specified range |
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| MA | Mask - image using circular mask |
| MA L | Mask - line across image |
| MA X | Mask - image in X direction |
| MA Y | Mask - image in Y direction |
| MA Z | Mask - image in Z direction |
| MD | Set Modes or options for operations |
| MK | Marker based alignment - Single tilted images |
| MK 3 | Marker based alignment - double tilted images |
| MM | Mask Multiplication |
| MM C | Mask Multiplication - Continuous |
| MN | Montage of Images |
| MN S | Montage of images - with individual Scaling |
| MO | Model image creation |
| MO 3 | Model volume creation |
| MR | Mirror image or volume |
| MS | Make empty inline Stack |
| MS 3 | Make empty inline volume Stack |
| MS F | Make empty inline Stack for Fourier images/volumes |
| MS I | Make empty indexed Stack |
| MS IF | Make empty Indexed Stack for Fourier files |
| MU | Multiply two or more, real or complex images |
| MU D | Divide real or complex files |
| MU M | Multiply 1st complex file by 2nd conjugated file |
| MU O | Multiply with arithmetic OR |
| MX | Maximum of image/volume |
| MY | User supplied subroutines |
| MY FL | Flush output to results file |
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| OD | Optical Density conversion |
| OP | Orientation of Projections in terms of Eulerian angles. |
| OR | ORientation search - half circle used |
| OR 2 | ORientation search - 2D || |
| OR 2M | ORientation search - 2D, multiple peaks || |
| OR 3A | ORientation search - 3D, Eulerian angles, arbitrary center || |
| OR 3Q | ORientation search - 3-D, Eulerian angles || |
| OR A | ORientation search - 2D, using self-correlation functions || |
| OR F | ORientation search - full circle used |
| OR FM | ORientation search - Full circle, Find > one peak |
| OR M | ORientation search - find More than one peak |
| OR MQ | ORientation search - resamples into polar coords, checks mirror || |
| OR NQ | ORientation search - resamples into polar coords. || |
| OR Q | Multireference alignment - based on self-correlation functions || |
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| PA | Patch image into a larger existing image/volume |
| PD | Pad Image/volume with borders |
| PDB CG3 | PDB - Calculate center of gravity |
| PDB IF | PDB - Find information |
| PDB PTS | PDB - Put coordinates in SPIDER document file. |
| PDB RT3 | PDB - Rotates PDB file in 3D space |
| PDB RT3A | PDB - Rotate PDB file by Euler angles around arbitrary center |
| PDB RT3L | PDB - Rotate PDB file around line |
| PDB SH | SHift coordinates in a PDB file |
| PDB STP | PDB - Create PDB file from coordinate list |
| PF | Profile an image row in a Postscript graph |
| PI REG | Output Register variable value on pipe |
| PJ 3 | Project - 3D volume |
| PJ 3O | Project - 3D volume (older version) |
| PJ 3Q | Project - 3D volume using Eulerian angles || |
| PJ 3Q O | Project - 3D volume using Eulerian angles (older version) || |
| PJ 3Q RR | Project - 3D volume using Eulerian angles & create rings file || |
| PJ AT | Project - 3D volume using exponential Attenuation |
| PJ COL | Projected Surface - Coloring |
| PJ CYL | Project - 3D volume onto Cylinder |
| PJ SHAD | Projected Surface - cosine Shading |
| PJ ST | Projected Surface - Creation |
| PK | Peak search |
| PK 3 | Peak search - 3D |
| PK 3D | Peak search - 3D, output to Document file |
| PK 3R | Peak search - 3D, Restricted neighborhood, output to Document file |
| PK C | Peak search - Center of gravity |
| PK D | Peak search - output to Document file |
| PK DC | Peak search - Center of gravity, output to Document file |
| PK DR | Peak search - Restricted neighborhood, output to Document file |
| PK M | Peak search - Maximum |
| PL | Plot Document file data into Postscript file |
| PL FIT | Fit Polynomial to Document file data |
| PL HI | Plot Histogram - from Document file |
| PO | Convert an image to polar coordinates representation. |
| PP | Put Points in image - from terminal |
| PP L | Put Points in image - from Document file Listing |
| PP LL | Put Lines in image - from Document file Listing |
| PP P | Put Points in image - from Document file, alters neighbors |
| PP V | Put height image into Volume |
| PS | Pick Slice - Y (xz planes) |
| PS A | Pick Slice - Arbitrary direction |
| PS X | Pick Slice - X, (yz planes) |
| PS Z | Pick Slice - Z, (xy planes) |
| PT | Create Pattern or mask file |
| PW | Amplitudes of Fourier transform |
| PW 2 | Power spectrum |
| PW L | Power spectrum - Log10 |
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| RA | Create Ramp image |
| RB 32F | Rotate, Shift, Sampled, Back Projection in Fourier space | |
| RB 3F | Rotate, Shift, Back Projection in Fourier space | |
| RC | Real Convolution || |
| RE | Return from procedure |
| RF | R Factor || |
| RF 3 | Phase Residual & Fourier shell correlation, 3D || |
| RF 3SN | 3D Spectral SNR of a 3D reconstruction || |
| RF SN | Spectral SNR of images || |
| RM | Radon transform suite of programs. |
| RM 2DN | Radon Transform - 2D |
| RM 3DN | Radon Transform - 3D |
| RM COMPLN | Radon Transform - 2D, Complete |
| RM FILTER | Radon Transform - Filter |
| RM FTINVN | Radon Transform - Inverse Fourier transform |
| RM FTN | Radon Transform - Fourier transform |
| RM INV2N | Radon Transform - Computes inverse (Fourier-)Radon transform |
| RM INV3N | Radon Transform - Computes inverse 3D (Fourier-)Radon transform |
| RM MAKE3 | Radon Transform - Create blank 3D Radon (or Polar Fourier) Transf. |
| RM RESET | Radon Transform - Clear counter and sigma |
| RM SUM3N | Radon Transform - Sum/average 2D Into 3D Fourier Radon transform |
| RO | Rotational average - single line output |
| RO I | Rotational average - 2D Image output |
| RP | Replace Pixel value |
| RR | Read Register variables |
| RR C | Read Register variables - Copy from global |
| RR G | Read Register variables - Global |
| RR S | Read Register variable - from list of variables |
| RT | RoTate - image or volume, use average as background |
| RT 3 | RoTate - volume, slow |
| RT 3A | RoTate - volume, arbitrary center, quadratic interpolation |
| RT 3AS | RoTate - volume, arbitrary center, simple interpolation |
| RT 3D | RoTate - volume, fast, quadratic interpolation |
| RT 3DS | RoTate - volume, fast, simple interpolation |
| RT 3L | RoTate - volume around an arbitrary line |
| RT 3LS | RoTate - volume around arbitrary line, simple interpolation |
| RT 90 | RoTate - image or volume, by 90, 180, or 270 degrees |
| RT B | RoTate - image or volume, supply Background |
| RT C | RoTate - image, around arbitrary center, for small files |
| RT M | RoTate - image or volume, use minimum as background |
| RT SQ | Rotate and Shift - image, Quadratic interpolation || |
| RTD SQ | Rotate and Shift - image, Quadratic interpolation || |
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| TF | Transfer Function - Defocus dependent |
| TF C | Transfer Function - Complex |
| TF C3 | Transfer Function - Complex 3D |
| TF CRF | Transfer Function - Determine Defocus & Amplitude contrast ratio |
| TF CT | Transfer Function - phase flipping, Complex, Binary |
| TF CT3 | Transfer Function - Complex, Binary 3D |
| TF CTS | Transfer Function - 2D & 3D CTF correction |
| TF CTS2 | Transfer Function - 2D CTF correction |
| TF D | Transfer Function - Display |
| TF DDF | Transfer Function - Determine DeFocus & amplitude contrast |
| TF DEV | Transfer Function - Determine Envelope function |
| TF DNS | Transfer Function - Determine and delete Noise background |
| TF ED | Transfer Function - Estimation of CTF parameters |
| TF L | Transfer Function - Send to document file |
| TF LM4 | Transfer Function - estimate image formation parameters |
| TF SIM | Transfer Function - Simulate an electron microscope image |
| TF SNR | Transfer Function - 3D CTF correction |
| TH | Threshold - Set pixels above/below Threshold to Threshold |
| TH C | Threshold - Change all pixels having a specific value in image |
| TH F | Threshold - Set pixels above/below Threshold to Fixed value |
| TH M | Threshold - Create Mask based on Threshold |
| TM | Elapsed Time |
| TP | Three dimensional Plot of image values |
| TT | Sets image Title |
| TT COPY | Copies image Title |
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