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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

@ 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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 ||

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 from 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 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 JPG Copy SPIDER file to a JPEG format
CP TO MRC Copy SPIDER file To MRC (CCP4) 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 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
CP TO XPLOR Copy SPIDER volume to X-PLOR format
CTF ED Contrast Transfer Function - Estimate Defocus from micrograph
CTF FIND Contrast Transfer Function - Estimation of CTF parameters
CV REPL Projection onto Convex sets - Replace projector
CYCLE Starts next loop iteration (Scripting operation)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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
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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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
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
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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 ||

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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. ||

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 ||

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 image 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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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 ED Transfer Function - Estimate Defocus from image power spectrum
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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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

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