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| @ | Invoke a procedure |
| @@ | Invoke a procedure without new namespace |
| 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 C | Alignment - multi-reference, rotation and Classification || |
| 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 - Reference free, Shift || |
| AP SCC | Alignment - multi-reference, translation alignment || |
| AP SH | Alignment - multi-reference, exhaustive rotation & shift ||* |
| AP SHC | Alignment - multi-reference, exhaustive rotation & shift ||* |
| AP SR | Alignment - reference free, Shift & Rotation || |
| AP TOOL | Alignment - Tool for evaluating parameters || |
| AR | Arithmetic operation |
| AR IF | Arithmetic operation on image - 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, Sampled, Interpolated in Fourier space ||* |
| BP 3D | Back Projection - 3D, using Euler angles || |
| BP 3F | Back Projection - 3D, Interpolated in Fourier space ||* |
| BP 3G | Back Projection - 3D, Gridded in Fourier space || |
| BP 3N | Back Projection - 3D, Nearest neighbor Interpolated in Fourier space || |
| BP CG | Back Projection - 3D, Iterative, Conjugate Gradients ||* |
| BP CG 3 | Back Projection - 3D, Sampled, Conjugate gradients ||* |
| BP R2 | Back Projection - Weighting 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 || |
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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 H | Cross Correlation - Phase || |
| 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 PH | Center of Gravity - Phase approximation || |
| CG SYM | Center of Object - Quasisymmetry Approximation || |
| CI | Confidence Interval |
| CL CLA | Classification - Diday's Clustering |
| CL HC | Classification - Hierarchical Clustering |
| CL HD | Classification - Hierarchical, get number of classes |
| CL HE | Classification - Hierarchical, create cluster selection files |
| 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 Old 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 RAW | Copy Raw Image to SPIDER file |
| CP FROM TERM | Copy Terminal input to SPIDER image/volume |
| 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 Byte Endian |
| CP TO POST | Copy SPIDER image to a POSTscript image |
| CP TO RAW | Copy SPIDER file to a 8-bit raw image |
| CP TO TIFF | Copy SPIDER file to a TIFF format |
| CP TO XPLOR | Copy SPIDER volume to X-PLOR format |
| CV REPL | Projection onto Convex sets - Replace projector |
| CYCLE | Starts next loop iteration (Scripting operation) |
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| DC | Decimate image/volume |
| DC S | Decimate image - Sum neighboring pixels |
| DE | Delete a file |
| DE A | Delete file series |
| DF | Density Foldover |
| DI | Dilate a binary image/volume |
| DI NF | Dilate an object - do not fuse objects |
| DN AD | Denoise - Anisotropic Diffusion |
| DN MED | Denoise - Median Filtering |
| DN MS | Denoise - Mean Shift |
| DO | Start of DO loop (Scripting operation) |
| DOC AND | "And" two Document files |
| DOC BOOT | Select Document file entries - randomly, with replacement |
| DOC COMBINE | Combine series of Document files. |
| DOC CREATE | Create Document file |
| DOC KEY | Re-Key Document file key numbers |
| DOC MERGE | Merge two Document files |
| DOC MIRROR | Mirror a Document file |
| DOC OLD | Copy new format Document file to Old format |
| DOC RAN | Randomly select Document file entries |
| DOC REN | Renumber Document file keys |
| DOC SHUFFLE | Shuffle Document file |
| DOC SORT | Sort Document file |
| DOC SPLIT | Split Document file into two Document files |
| DOC STAT | Get Statistics from column in Document file |
| DOC SUBTRACT | Subtract two Document files |
| DR DIFF | Density Reference - Error & Difference between two volumes |
| DR ERR | Density Reference - Error between two volumes |
| DU | Dust removal |
| DU V | Dust removal - specify value for removed pixels |
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| EC CL | Extract Connected Clusters |
| EC CLOSE | Extract Connected Clusters - merge close clusters |
| EC FILTER | Extract Connected Clusters - Filter |
| EC SELECT | Extract Connected Clusters - Selection |
| EC STAT | Extract Connected Clusters - Statistics |
| ED | Edge Detection |
| ELSE | Conditional execution of operations (Scripting operation) |
| ELSEIF_THEN | Conditional execution of operations (Scripting operation) |
| EN | End SPIDER session |
| EN D | End SPIDER session - Delete Results file |
| ENDDO | End of DO loop (Scripting operation) |
| EP | Error Probability |
| EP TM | T test - Each Point |
| EP TT | T test |
| ER | Erode a binary image/volume |
| ER DOC | Erode binary image/volume - Save UEP in doc file. |
| ER EDM | Create Euclidean Distance Map |
| ER SK | Erode a binary image to make skeleton |
| ER WA | Erode image to a "watershed" |
| EV | Set system environmental variable |
| EXIT | Ends execution of current operation loop (Scripting operation) |
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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 - List and retrieve file header value(s) by location |
| FI A | File Information - Multiple files |
| FI H | File Information - Retrieve file Header values by name |
| FI N | File Information - Do not halt if file not found |
| FI X | File Information - Retrieve file header value(s) by location |
| FP | Interpolate/Resize using Fourier transform || |
| FQ | Filter - Quick Fourier, High, low pass, etc. || |
| FQ NP | Filter - Quick Fourier, High, low pass, etc, No Padding || |
| FR | Read (sets) a local string (symbolic) variable |
| FR F | Read (sets) global symbolic (string) variables from a file |
| FR G | Read (sets) a global string (symbolic) variable |
| FR GS | Sets global string variable using current string values |
| FR L | Read (sets) a local string (symbolic) variable |
| FR LS | Sets local string variable using current string values |
| FR N | Read (sets) next global symbolic (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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| IA | Interface Area |
| IF | Conditional expression execution (Scripting operation) |
| IF_GOTO | Conditional jump (Scripting operation) |
| IF_THEN | Conditional execution of operations (Scripting operation) |
| IN | Insert - image into a larger existing image |
| IN S | Insert - image and contrast Stretch |
| IP | Interpolate/Resize using bilinear/trilinear interpolation |
| IP FS | Interpolate/Resize - using Fourier based bicubic spline || |
| IP FT | Interpolate/Resize - using Fourier Transform || |
| IP T | Interpolate/Resize - using Triangular interpolation |
| IQ DIR | Inquire if a directory exists |
| IQ FI | Inquire if a file exists |
| IQ GONE | Wait until a file is gone |
| IQ PID | Inquire current Process ID |
| IQ REG | Inquire if a Register variable's value is correct |
| IQ SYNC | Wait until a file exists |
| IQ SYNC D | Wait until a file exists then delete it |
| IQ VER | Inquire number of current SPIDER version |
| IQ WO | Inquire values within raw files |
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| MA | Mask - image/volume with a 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 two images/volumes |
| MY | User supplied subroutines |
| MY FL | Flush output to results file |
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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 for single projection |
| PJ 3F | Project - 3D volume using Eulerian angles || |
| PJ 3G | Project - 3D volume using Gridding by Eulerian angles || |
| PJ 3Q | Project - 3D volume using Eulerian angles || |
| 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 image file |
| PW | Amplitudes of Fourier transform |
| 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 | Fourier Ring correlation 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 |
| ROT | ROTate image/volume around center by specified angle(s) |
| ROT A | ROTate around arbitrary center |
| ROT L | ROTate volume around specified line |
| RP | Replace Pixel value |
| RR | Read (Set) 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 90 | RoTate - image or volume, by 90, 180, or 270 degrees |
| RT SF | Rotate and Shift - image, Fourier based spline interpolation || |
| RT SQ | Rotate and Shift - image, Quadratic interpolation || |
| RTD SF | Rotate and Shift - image, Fourier based spline interpolation || |
| RTD SQ | Rotate and Shift - image, Quadratic interpolation || |
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| SA | Sum Alignment |
| SA 3 | Sum Alignment in 3D |
| SA E | Sum Eulerian angles |
| SA P | Sum Alignment - Positive rotation and shift |
| SD | Save Document |
| SD C | Save Document - from CA S (_IMC) file |
| SD E | Save Document - End |
| SD IC | Save Document - In Core |
| SD IC COPY | Save Document - In Core, Copy |
| SD IC NEW | Save Document - In Core, create New storage array |
| SD SHUFFLE | Shuffle Document file |
| SE | Seed fill an image |
| SH | Shift - using bilinear/trilinear interpolation || |
| SH F | Shift - using Fourier interpolation || |
| SK | Stack images into volume |
| SK R | Replace a slice in volume |
| SL | Create slice through image series |
| SN RB | SNR Butterworth |
| SN RF | SNR Filter |
| SO | Surface extraction |
| SO C | Surface Comparision |
| SP | Find info on diffraction pattern spots |
| SQ | Square image values |
| SQRT | Square root of image/volume |
| ST | Set values in image header |
| ST H | Set values in image/volume Header by name |
| SU | Subtract images/volumes |
| SY DOC | Create Symmetry Document file |
| SZ | Squeezes (Shears) an Image |
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| TF | Transfer Function - Defocus dependent |
| TF C | Transfer Function - Complex 2D |
| TF C3 | Transfer Function - Complex 3D |
| TF COR | Transfer Function - CTF correction and back transfom |
| TF CRF | Transfer Function - Determine Defocus & ACR |
| TF CT | Transfer Function - phase flipping, Complex, Binary |
| TF CT3 | Transfer Function - Complex, Binary 3D |
| TF CTS | Transfer Function - 2D & 3D 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 RCTF | Transfer Function - Rotational average? |
| TF SIM | Transfer Function - Simulate an electron microscope image |
| TF SNR | Transfer Function - 3D CTF correction, Freq. dependent snr |
| 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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