SPIDER: Task Index

The links listed below usually point to one or two examples of a set of operations. For example, there are several operations related to alignment with different suboptions under AP. The remaining operations can be found under See Also on the linked AP SH page. In many cases image refers to either a 2D image or a volume. See the Glossary for definitions of unknown terms.

Add: A whole image series AS; Series of two images ADD 2; Two images ADD; Images of different size PA; Value to each pixel AR; Image into larger image PA
Anisotropic diffusion CE AD
Align images AP SHC, AP REF, & AP SA: Reference-free info; Reference-based info
Arithmetic pixel-by-pixel operations AR
Autocorrelation AC
Average: Series of images AS; Rotational RO
Back-projection BP 3D & BP W2
B-Factor filtration FQ & FQ NP&
Binary image: Creation TH F & TH M; Enlarge (dilate) a binary object DI; Erode a binary object ER
Blank image creation BL
Blowup (enlarge) an image IP
Box convolution BC
CCP4 file creation CP TO MRC
Center object using phase approximation CENT PH
Center of gravity CG, CG 3, & CG PH
Change file extension NC
Check value in a register IQ REG
Classification CL HC, CL KM, CL CLA, see also: Classification
Cluster determination & extraction EC CL
Colored suface PJ COL
Confidence interval CI
Contrast enhancement CE ST
Contrast normalization: Linear ramp subtraction RA; Gaussian fit and subtraction RA GN
Contrast transfer function TF
Copy SPIDER files CP
Copy image files from other formats to SPIDER format: From CCP4 CP FROM MRC; From EMISPEC CP FROM EMI; From MRC CP FROM MRC; From Nikon TIFF file CP FROM NIK; From PDB CP FROM PDB; From RAW CP FROM RAW; From X-PLOR ASCII CP FROM XP
Copy SPIDER format image files to other formats: To BRIX "O" CP TO BRIX; To CCP4 CP TO CCP4; To MRC CP TO MRC; To opposite byte ordering CP TO OPEND; To Postscript CP TO POST; To raw CP TO RAW; To TIFF CP TO TIFF; To X-PLOR CP TO XPLOR
Copy in-core doc file to disk SD IC COPY
Contour an image: Into Postscript file CO; Into SPIDER image FC
Contrast Transfer Function: Generation TF C & TF C3; Correction TF COR & TF CTS; Defocus determination CTF ED & CTF FIND & TF ED
Convolution CN, RC, BC, see also: Web
Correspondence analysis CA S, BC, see also: Multivariate data analysis
Create: Binary image TH M; Blank image BL; Contrast transfer function TF C; Lines in image PP LL; Labels (text) in image LA; Points in image PP; Mask PT; Model image MO; Model volume MO 3; Ramp RA; Stack file MS; Symmetry doc file SY DOC
Cross-correlation CC
Cross-correlation coefficient CC C
Decimate (reduce size of) image DC, IP
Defocus: Determination CTF ED, TF ED, & CTF FIND; Display TF D
Delete: File DE; Series of files DE A
Density foldover (multiple linear density mapping) DF
Denoise: Using anisotropic diffusion DN AD; Using median filter DN MED; Using mean shift filter DN MS
Dilate (enlarge) a binary image DI
Divide: Series of images by another DIV 2; Image by another DIV; Image pixels by constant value AR
Document files: Logical "and" two doc files DOC AND; Create DOC CREATE; Find non existing values in DOC MIRROR; Find max value in UD MAX; Graph contents using Postscript PL; Histogram of contents HD D; List contents LD; Merge two doc. files DOC MERGE; Merge series of doc. files DOC COMBINE; Randomly select values from DOC RAN; Renumber DOC REN; Retrieve info from UD N; Save registers in SD; Shuffle SD SHUFFLE; Sort DOC SORT; Split DOC SPLIT; Statistics DOC STAT; Subtract two doc files DOC SUB
Distance map ER EDM
Do-loop: End LB#
Dust removal (remove out-lying values) DU, CE MED
Edge detection: Frei-Chen filter CE FREI; Laplacian filter CE LAP; Prewitt filter CE P; Sobel filter CE SOBEL; Weiner filter ED; Local orientation filter CE OR
End SPIDER session EN
Enlarge an image IP, FP
Enlarge (dilate) a binary object DI
Erode a binary object ER
Error probability EP: Error between 2 volumes DR ERR; Error and difference between 2 volumes DR ERR
Euclidean distance map from image ER EDM
Eulerian angles:: Generate equispaced angles VO EA; Combine angles SA, SA 3 & SA P; Rotate angles VO RA & SA P
Exit SPIDER session EN
Export non-SPIDER images ... See: copy to
Factor map display CA SM or SD C then Web
File: Check existance IQ FI; Information FI; Check header values FI H; Set header values ST H; Statistics (min, max, etc) FS; New extension NC; Wait for creation IQ SYNC
Filter: Box BC; Convolution CN; Design FF PLOT; Fourier FF & FQ; Frei-Chen CE F; Haralick CE HAR; Laplacian CE LAP; Maximum CE MAX; Median CE MED; Minimum CE MIN; Prewitt CE P; Sobel CE SOBEL; Top-hat CE TOP; Using doc file FD
Find: Minimum and maximum of an image FS; Statistics of an image FS; An image header value FI X, FI H, LI T; Resolution criterion RF
Fourier: Filter FF & FQ; Filter design FF PLOT; Helical Fourier HF; Interpolation (by padding with zeros) FP; Inverse transform FT; Ring correlation FRC & RF; Shell correlation FSC & RF 3; Transform FT; Reconstruction BP 3F
Flush results file MY FL
Frei-Chen filter CE FREI
Gallery creation (montage) MN, see also: Web
Go to (inside procedure) GO TO & LB#
Gradient of image CE G
Graph ... See: plot
Helical Fourier HF
Header variables: Setting ST H; Querying FI H
High-pass filtration: Fourier filtration FT, FF- FT; Quick Fourier filtration FQ
Histogram: Of image HI or Web; Equalization of image CE HI; Local area histogram equalization of image CE LAHE; Of doc file PL HI
If IF, IF..THEN, & IF..GOTO
Interpolate (i.e. resize by sampling) image IP, IP T, IP FT, & IP FS
Import non-SPIDER images ... See: copy
Image header statistics: Displaying FS; Setting ST
Insert image into another, larger one IN
Intensity of a spot SP
Interfacial area IA
Invert contrast or (negate) an image NEG & AR
Label LB
Laplacian filter CE LAP
Lattice indexing (from power spectrum) WT
List: Image (pixel) values LI; Doc file contents LD
Local area histogram equalization CE
Logical if IF
Low-pass filtration: Box convolution BC; Fourier filtration FT, & FF FT; Quick Fourier filtration FQ
Make ... See: create ...
Marker fit (single-tilt reconstruction) MK
Mask MA: Creation PT & MO; Creation using threshold TH M; Multiplication MM; Soft edged MA SOFT
Maximum: Filter CE MAX; Of image FS
Median filter CE MED
Menu of operations SPIDER Menu
Minimum: Filter CE MIN; Of image FS
mirror (create mirror-related image) MR
Mode (global settings switch) MD
Model (create model distributions in 2D and 3D) MO & MO 3
Montage (put images into gallery) MN see also: Web
MRC image creation CP TO MRC
Multiply: Series of two images MUL 2; Two images MUL; Image pixels by a value AR; Image with mask MM; Complex-valued (Fourier) files MUL
Multi-variate statistics CA S, see also: Multivariate statistical Analysis
Negate (invert) an image NEG & AR
New data code (file extension) NC
Non-linear mapping of MSA coordinates onto 2D plane CA MAP
Optical density conversion OD

Orientation search OR 2, OR 3 & OP
Pad image into larger frame PD
Particle picking (automatic) AT PK, AT WN, AT IT & AT SA
Patch (add) image into larger image PA
Patch averaging WV
Pattern (create pattern using single pixels) PT
PDB files: Converting to SPIDER CP FROM PDB; File information PB IF; Rotation PB RT3; Shift PB SH; Convert coordinates PB PTS
Peak search PK & PK M
Phase residual (differential) RF
Pick slice (from a volume) PS
Pixel value: Listing GP & LI T; Setting RP
Plot: Doc. file contents into Postscript file PL; Histogram from doc. file into Postscript file PL HI; Image row into Results file GR; Image col. or row into Postscript file PF; Three-dimensional (perspective) TP
Polar coordinates PO
POCS (projection onto convex sets) CV REPL
Power spectrum: From Fourier transform PW; Lattice indexing WT
Prewitt filter CE P
Principal component analysis (PCA) CA S
Processors (set number of) MD
Project PJ 3
Put See also: set ...: Pixels in image PP, PT or Web; Lines in image PP L
Radon transforms RM
Ramp creation RA
Range image CE RANGE
Read register RR, RR S, Assignment, & Guide
Reconstitute images CA SR, CA SRD
Reconstruction ... See back projection
Register variable usage: Checking values IQ REG; Set pipe for register values MD /PIPE; Pipe register value PI REG; Setting values RR, RR S, Assignment, & Guide
Replace slice by an image SK R
Replace pixel value in image RP
Resize image IP, FP & DC
Resolution criterion (by comparing Fourier transforms) RF
Results file: Canceling MD /NO RESULTS; Decreasing length MD /VB OFF; Flush MY FL
Return (from procedure) RE
R-Factor RF
Ridge image CE RIDGE
Rotate image RT
Rotational alignment AP REF, AP SH & AP RA
Rotational average RO SD
Save in document file: Selected register variables SD; MSA coordinates SD C; Histogram from doc. file HD D; Image values LI D; Peak locations PK; Polynomial curve PL FIT
Seed fill SE
Segmentation : edge detection , filter, texture segmentation , EC CL & ER EDM
Set: A pixel value in image RP; Image header value ST; Image title TT; New file extension NC; Number of processors MD / SET PROCS; Number of registers MD / SET REGS; Pipe for register variables MD / PIPE; Random number generator seed MD / SET SEED; Register variables Assignment & Guide; System environment variables EV; Symbolic variable Assignment, Guide & FR
Shear image SZ
Shift: Shift image SH; Shift volume SH 3
Shift alignment AP SA
Shrink image IP, DC & FP
Shrink to threshold SK
Signal to noise ratio (SNR) RF
Skeleton of binary image ER SK
Slice a volume PS
Slice (by row) from a series of images SL
Sobel filter CE SOBEL
Sort document file DOC SORT
Square (multiply image with itself) SQ
Square root (take square root of each pixel) SQRT
Stack file creation MS
Stack images into a volume SK
Statistics of an image FS
Sub-sample an image IP
Subtract: Series of two images SUB 2; Two images SUB; Value from each image pixel AR
Sum alignment (2D vectorial additions of rotations and shifts) SA
Surface representation of volume PJ ST better yet: Web
Surface shading of volume PJ ST, PJ SHAD better yet: Web
System call VM
Symmetry doc file creation SYDOC
Text: Place in image LA or Web; Place in image title TT
Texture segmentation: Hurst operator CE HURST; Maximum CE MAX; Minimum CE MIN; Range CE RANGE; Ridge CE RIDGE; Variance CE VAR
Top-hat filter CE TOP
Three-dimensional plot (perspective plot) TP
Threshold image: Image TH; Image and produce binary mask file TH M
Tilt axis determination DC
Time elapsed since last call TM
Title (add title to SPIDER file) TT
Transfer function TF
T-test EP TT
Unsave document file values UD
User supplied routines MY
Variance: Of an image series AS; Of an image FS; Image CE VAR; Of reconstruction VA F
Vectorial additions of angles in doc file VO
Wait for a file IQ SYNC
Window (select small area from image) WI, see also: Web
Window averaging (average unit cell repeats within patches) WV
Warp an image WA
Watershed: Erode to watershed ER WA; Watershed image CE WA

CROSS-REFERENCE INDEX