## MANUAL OF SPIDER OPERATIONS

Use the Cross-Reference Index to find operation for a desired task. A || symbol indicates the operation contains OMP parallel directives. A ||MPI symbol indicates the operation contains both OMP and MPI parallel directives. See also: SPIDER's Pocket Calculator

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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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 GOTO GOTO (Scripting operation) GP Get Pixel value GR Graph an image row - in Results file GR T Graph an image row - on Terminal

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 HD Histogram of Document file column HD R Histogram of Document file column - use specified range HI E Histogram - to determine entropy HI JOINT Histogram - Joint, to determine mutual shared information HIS Histogram - image/volume HIS R Histogram - Image/volume, Restricted 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 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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 LA Add text label below an image LA L Put text label inside an image LB# Label for jump operation or end of DO-loop (Scripting operation) LI List image values - in Results file LI D List image values - in Document file LI T List image values - on terminal LI X List image values - in register variables LO Locate motif inside a search volume LO I Initialize files for Locating motif inside volume LO LSD Prepare LSD volume for Locating motif inside volume

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 NC New data/project file extension NEG Negate - invert contrast of image NEG A Negate - invert contrast of image & preserve average NORM Normalization of image/volume using average and deviation ||

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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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 UD Unsave Document UD E Unsave Document - End UD FIND Unsave Document - Find value UD FIND E Unsave Document - End Use of UD Find incore doc UD IC Unsave Document - In-core, Retrieve register values UD ICE Unsave Document - End use of In Core document file UD MAX Unsave Document - get Max/Min from document column UD N Unsave Document - get key Numbers from file UD NEXT Unsave Document - Next line UD NEXT E Unsave Document - End UD S Unsave Document - Sequential search

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 VA 3Q Bootstrapping method for variance estimation VA 3R Variance estimation VA F Variance of reconstruction in Fourier space as function of frequency || VAR Variable Assignment VM System call VO EA Vector Operation - Create Doc File Containing Evenly Spaced Angles VO EPT Vector Operation - Euler angle point rotation VO IA Vector Operation - Find Included Angle VO MD Vector Operation - angular Document file from 'AP MD' output VO MQ Vector Operation - create selection files from 'AP' output VO NEA Vector Operation - Create More Uniformly Spaced Angles VO RA Vector Operation - Rotate Angular doc file VO RAS Vector Operation - Rotate Angular doc file & Set angle

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 WA Warp an image/volume WI Window image/volume WI B Window image - use specified Background WV Window averaging WV P Window averaging - over Patches WV S Window averaging - Sequential document search
 XM MA Create Xmipp selfile XM S2D Convert Star file to SPIDER doc file