CROSS-REFERENCE 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 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 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/ FILTER
Correspondence analysis   CA S,   BC, see also:   Multivariate data analysis
Create
Binary image   TH M
Blank image   BL
  TH M
Contrast transfer function   TF C
  TH M
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
Start   DO
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   VO CEUL
Rotate angles   VO RA
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 / MONTAGE
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 see also:   WEB/ HISTOGRAM
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 / MONTAGE
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
Labels in image   WEB / TEXT - / RECORD SCREEN
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
Surface shading of volume   PJ ST,   PJ SHAD better yet:   WEB/ SURFACE
System call   VM
Symmetry doc file creation   SYDOC

Text
Place in image   LA
Place in image   WEB / TEXT - / RECORD SCREEN
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
Window averaging (average unit cell repeats within patches)   WV
Warp an image   WA
Watershed
Erode to watershed   ER WA
Watershed image   CE WA

Source: crossref.html     Last update: 22 Jan. 2018     ArDean Leith
© Copyright Notice /       Enquiries: spider@wadsworth.org