| @ | 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 S | Add Series of images |
| ADD | Add images |
| ADD 2 | Pairwise add series of real or complex images |
| ADD F | Add two images with factors |
| ADD R | Add two images with ratio |
| AP C | Rotation Alignment - classification, unknown references || |
| AP I | Alignment - Initialize Rings File || |
| AP MS | Alignment - multi reference, shift || |
| AP RA | Alignment - Reference free, Rotation || |
| 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, fast 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 F | Average images - find statistics & Q factor map || |
| AS R | Average image/volume series, optional subset |
| AS S | Average image/volume series, optional subsets, select outputs |
| AT IT | Automatic particle picking - sort doc file |
| 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/volume |
| 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 3F MERGE | Back Projection - 3D, Interpolated in Fourier space, Merge || |
| BP 3F PART | Back Projection - 3D, Interpolated in Fourier space, Partial || |
| 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, Iterative, sampled, Conjugate gradients ||* |
| BP R2 | Back Projection - Weight image series || |
| BP RP | Back Projection - 3D, iterative, Richardson, constrained ||* |
| BP RP 3 | Back Projection - 3D, iterative, Richardson, constrained ||* |
| BP S2 | Back Projection - 2D, single tilt, iterative, constrained || |
| BP W2 | Back Projection - 2D, filtered, weighted || |
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| CA NOISE | Correspondence Analysis - Create Eigenvalue doc file for noise |
| 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 | Contrast Enhancement - Histogram Stretching |
| 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 |
| CENT PH | Center image/volume using phase approximation |
| CG | Center of Gravity |
| CG PH | Center of Gravity - Phase approximation || |
| CG SYM | Find center of Object - Quasi-symmetry Approximation || |
| CI | Confidence Interval |
| CL CLA | Classification - Automatic |
| CL HC | Classification - Controlled |
| CL HD | Classification - Hierarchical, get number of classes |
| CL HE | Classification - Hierarchical, create cluster selection files |
| CL KM | Classification - K Means || |
| CN | Convolution || |
| CN N | Convolution - Normalized || |
| CO | Contour image/volume into Postscript file |
| CP | Copy SPIDER file to SPIDER file |
| CP FROM ASCII | Copy ASCII text file to SPIDER file |
| CP FROM EMI | Copy EMISPEC format file to SPIDER file |
| CP FROM MRC | Copy MRC 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 TIF | Copy TIFF format file to SPIDER file |
| CP FROM VAX | Copy VAX SPIDER file to a Unix 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 JPG | Copy SPIDER file to a JPEG format |
| CP TO MRC | Copy SPIDER files To MRC format files |
| 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 STK | Copy a series of stacks into a single new stack CP TO STK |
| CP TO TIFF | Copy SPIDER file to a TIFF format |
| CP TO VOL | Copy images into volume |
| CTF FIND | Contrast Transfer Function - Estimation of CTF parameters |
| 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 (enlarge) object in a binary image/volume |
| DI NF | Dilate an object - do not fuse objects |
| DIS | Display single image using ImageMagick |
| DIS REL | Display image(s) using Relion_display |
| DIV | Divide real or complex files |
| DIV 2 | Pairwise divide series of real or complex images |
| DN AD | Denoise - Anisotropic Diffusion |
| DN MED | Denoise - Median Filtering |
| DN MS | Denoise - Mean Shift |
| DO | Start of a 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 PLOT | Plot Document file data using Gnuplot |
| DOC RAN | Randomly select Document file entries |
| DOC REN | Renumber Document file keys |
| DOC SEP | Seperate a Document file into multiple files |
| DOC SHUFFLE | Shuffle Document file |
| DOC SLICE | Put slice from document file into new document file |
| DOC SORT | Sort Document file |
| DOC SPLIT | Alternately 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 |
| 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 object in a binary image/volume |
| ER EDM | Create Euclidean Distance Map |
| ER SK | Erode object a binary image to make its 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 | Fourier filter image/volume according to a Document file || |
| FD C | Fourier filter image/volume according to specifed column of Document file || |
| FF | Filter - Fourier |
| FF PLOT | Fourier - Filter design |
| FI | File Information - List and retrieve file header value(s) by location |
| FI A | File Information - Multiple files |
| FI CEN | File Information - report image/volume center |
| FI H | File Information - Retrieve file Header values by name |
| FI N | File Information - List and retrieve, No halt if file not found |
| FP | Interpolate/Resize using Fourier transform || |
| FQ | Filter - Quick Fourier, High, low pass, etc., Padded || |
| FQ NP | Filter - Quick Fourier, High, low pass, etc, No Padding || |
| FR | Read (sets) a local string variable |
| FR F | Read (sets) global string variables from a file |
| FR G | Read (sets) a global string variable |
| FR GS | Sets global string variable using current string values |
| FR L | Read (sets) a local string variable |
| FR LS | Sets local string variable using current string values |
| FR N | Read (sets) next global string variable from file |
| FRC | Fourier ring correlation and resolution determination || |
| FS | Find Statistics |
| FS LOC | Find Statistics - location of min & max pixels |
| FS M | Find Statistics - within Mask |
| FS VAL | Find Statistics - location of valleys and ridges |
| FSC | Fourier shell correlation and resolution determination || |
| FSC NEW | Fourier shell correlation and resolution determination || |
| FT | Fourier Transform || |
| FT R | Fourier Transform Replace |
| FV | Find threshold for Volume |
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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 image |
| IN S | Insert - image into a larger image and contrast Stretch |
| IP | Interpolate/Resize using bilinear/trilinear interpolation |
| IP FS | Interpolate/resize image/volume - using Fourier based cubic spline || |
| IP FT | Interpolate/Resize - using Fourier Transform || |
| IP T | Interpolate/Resize - using Triangular interpolation |
| IQ COMP | Inquire which compiler was used for this SPIDER |
| IQ DIR | Inquire if a directory exists |
| IQ FI | Inquire if a file exists |
| IQ GONE | Wait until a file is gone |
| IQ PAR | Inquire if a string variable's value is correct |
| 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/volume |
| MA SOFT | Mask - image/volume with a soft adaptive mask || |
| MA X | Mask - image/volume in X direction |
| MA Y | Mask - image/volume in Y direction |
| MA Z | Mask - volume in Z direction |
| MD | Set Modes or options for operations |
| MD MRC | Set Modes or options for MRC related operations |
| MK | Marker based alignment - single tilted images |
| MK 3 | Marker based alignment - double tilted images |
| ML | Multiple linear regression for frame alignment |
| MM | Mask Multiplication |
| MM C | Mask Multiplication - Continuous |
| MN | Montage of Images |
| MN S | Montage of images - with individual Scaling |
| MO | Create Model image |
| MO 3 | Create Model volume |
| MR | Mirror image or volume |
| MRC HE | List values in MRC data file header |
| 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 |
| MUL | Multiply two or more, real or complex images |
| MUL 2 | Pairwise multiply series of real or complex images |
| MUL M | Multiply 1st complex file by 2nd conjugated file |
| MUL 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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| OD | Optical Density conversion |
| OP | Orientation of Projections in terms of Eulerian angles. |
| OR 3A | ORientation search - 3D, Eulerian angles, arbitrary center || |
| OR 3Q | ORientation search - 3D, Eulerian angles || |
| OR A | ORientation search - 2D, uses self-correlation || |
| OR MAP | ORientation MAP - 2D, rotational cross correlation plot || |
| OR Q | ORientation search - 2D, multireference, rotation & translation, uses self-correlation || |
| OR R | ORientation Search - 2D, rotation, uses polar coords. || |
| OR SH | Orientation Search - 2D, rotation & shift, uses polar coords. || |
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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 - Rotate by Euler angles in 3D space |
| PDB RT3A | PDB - Rotate by Euler angles around arbitrary center |
| PDB RT3L | PDB - Rotate PDB file around line |
| PDB SH | PDB - SHift coordinates |
| PDB STP | PDB - Create PDB file from coordinate list |
| PF | Profile an image row in a Postscript graph |
| PF G | Profile an image row in a Gnuplot graph |
| PI REG | Output Register variable value on pipe |
| PJ 2 | Project - 2D volume onto line |
| PJ 3 | Project - 3D volume using Eulerian angles, trilinear or FBS interpolation, single projection |
| PJ 3F | Project - 3D volume using Eulerian angles, FBS interpolation || |
| PJ 3G | Project - 3D volume using Eulerian angles, Gridded interpolation || |
| PJ 3Q | Project - 3D volume using Eulerian angles, trilinear interpolation || |
| PJ 3Q RR | Project - 3D volume using Eulerian angles & create rings file || |
| PJ CYL | Project - 3D volume onto Cylinder |
| PK | Peak search |
| PK 3D | Peak search - 3D, output to Document file |
| PK 3R | Peak search - 3D, Restricted neighborhood, output to Document file |
| PK D | Peak search - 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 Doc file |
| PO | Convert image to polar representation - rays along Y. |
| PO R | Convert image to polar representation - rays along X |
| 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 |
| PW | Power spectrum - Amplitudes of Fourier transform || |
| PW L | Power spectrum - Log10 || |
| PW PH | Phase spectrum || |
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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 | Phase Residual & Fourier ring correlation, 2D || |
| RF 3 | Phase Residual & Fourier shell correlation, 3D || |
| RF 3SN | 3D Spectral SNR of a 3D reconstruction || |
| RF SN | Spectral SNR of images, resolution determination & integral SNR || |
| RI R | Find vertical ridges running up/down an image |
| RI RV | Find ridges and valleys running up/down an image |
| RM | Radon transform suite of operations. |
| RO I | Rotational average - 2D Image output |
| RO SD | Rotational average - single line output, doc file |
| ROT | ROTate image/volume around center by specified angle(s) |
| ROT A | ROTate image/volume around arbitrary center |
| ROT L | ROTate volume around specified line |
| RP | Replace Pixel value |
| RR | Read (Set) Register variables |
| RR C | Read Numeric (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 SF M | Rotate, Shift & Mirror - image, Fourier based spline interpolation || |
| RT 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, Save registers |
| SD IC COPY | Save Document - In Core, Copy to Disk |
| SD IC NEW | Save Document - In Core, create New storage array |
| SD ICE | Save Document - In Core, End |
| SE | Seed fill an image |
| SH | Shift - using bilinear/trilinear interpolation || |
| SH F | Shift - using Fourier interpolation || |
| SK | Stack images/volumes 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 |
| SPH DECON | Spherically deconvolute a volume |
| SQ | Square image values |
| SQRT | Square root of image/volume |
| ST | Set values in data file header |
| ST H | Set values in image/volume Header by name |
| SUB | Subtract images/volumes |
| SUB 2 | Pairwise subtract series of real or complex images |
| SY DOC | Create Symmetry Document file |
| SYS | System call |
| SZ | Squeezes (Shears) an Image |
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| TF | Transfer Function - Generate image showing effect of defocus on CTF |
| TF C | Transfer Function - Generate a straight, complex, CTF correction image |
| TF C3 | Transfer Function - Generate a straight, complex, CTF correction volume |
| TF COR | Transfer Function - CTF correction, image/volume |
| TF CRF | Transfer Function - Determine Defocus & ACR |
| TF CT | Transfer Function - Generate a binary, phase flipping, complex, CTF correction image |
| TF CT3 | Transfer Function - Generate a binary, phase flipping, complex, CTF correction volume |
| TF CTS | Transfer Function - CTF correction with SNR, image/volume |
| TF D | Transfer Function - Generate image showing effect of astigmatism on CTF |
| TF DDF | Transfer Function - Determine Defocus & amplitude contrast |
| TF DEV | Transfer Function - Determine Envelope function |
| TF DNS | Transfer Function - Delete noise background |
| TF L | Transfer Function - Generate CTF, in doc file |
| TF LIS | Transfer Function - Generate phase flipping, binary CTF, in doc file |
| TF LM4 | Transfer Function - Determine CTF envelope B-factor and noise parameters |
| TF SIM | Transfer Function - Simulate an electron microscope image |
| TF SNR | Transfer Function - CTF correction, using frequency 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 | Set image Title |
| TT COPY | Copy image Title |
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