WHAT'S NEW IN SPIDER

Important changes in SPIDER operations are listed here.

Note that these changes may NOT be in the release of SPIDER that you have at your site. You may have to download a more recent release.

End of support for: SGI Irix and SGI Linux (on ALtrix)

We will cease compiling for SGI Irix and SGI Linux with this release. Our machines are too old to continue (RIP).

3/14/08 AL

SPIDER executables for Linux and Altix now use FFTW3.: In SPIDER single threaded FFTW3 Fourier transforms are often slightly slower than FFTW2 transforms. However multiple threaded FFTW3 transforms are significantly faster than our FFTW2 implementation. Since multi-processor machines are now common we have switched to FFTW3. The MD operation has been altered to allow controlling number of FFTW3 threads.; 12/14/07 AL
Web for use on Intel based OSX: We now supply executables for X-Window Web for use on Intel based OSX. Thanks to Dr. Ngai Shing Mogk and Dr. Neil Ranson from the University of Leeds for modifying Web for use on OSX.; 11/30/07 AL
TH, TH C, TH F, & TH: Operations return optional register variable containing number of pixels affected.; 10/09/07 AL
SPIDER for Intel based OSX systems: Makefile and executable for OSX on Intel are supplied.; 04/24/07 AL
OP: This operation can now use a selection document file to pick input files to operate on.; 1/20/07 AL
UD NEXT: New operation for sequentially accessing document files.; 2/20/07 AL
RB 3F & RB 32F: New operations which combine 'RT SQ and 'BP 3F' or 'BP 32F' for increased speed when used with stacks.; 1/10/07 AL
RT SQ: This operation can now use a selection document file to pick which input files to operate on.; 1/10/07 AL
CYCLE & EXIT: New operations for controlling iteration execution in SPIDER DO Loops.; 11/09/06 AL
ELSEIF: New operation for controlling conditional execution in SPIDER procedures.; 11/07/06 AL
ENDDO & DO: New syntax for ending a SPIDER 'DO' loop.; 11/07/06 AL
FR N: New operation reads symbolic parameters one-by-one from variable list file.; 11/03/06 AL
Symbolic Parameters
Symbolic parameters are now true string variables. They can be assigned new values at any time.: 11/02/06 AL
DO: Added optional loop index increment.; 10/25/06 AL
VO NEA: New operation creates angular document file which provides more 'uniform' coverage than 'VO EA'. Uses a logarithmic spiral for spacing the angles.; 10/12/06 AL
HD, HD D, & HD R: Operations have additional queries to set number of bins in histogram.; 10/02/06 AL
RR S: New operation to read value(s) from a list of values into a register variable(s).; 04/04/06 AL
DOC BOOT: New operation to select document file entries randomly with replacement.; 01/20/06 AL
CP TO CCP4: Operation has additional queries to set cell dimensions.; 01/10/06 AL

2005

Global register variables: Can now create "global register variables" using RR G which can be copied into current procedures using RR C.; 12/29/05 AL
Names for registers: SPIDER users can now specify names for register variables instead of using predefined "x11 ,x12,..." names.; 12/10/05 AL
Precompiled Linux executables with FFTW: Precompiled SPIDER Linux executables distributed with SPIDER are now statically linked with FFTW libraries.; 09/28/05 AL
Copyright: SPIDER/Web released under GPL license.; 09/18/05 AL
DOC KEY: New operation creates a selection document file from a document file having non-consecutive keys.; 07/30/05 AL
UD IC: Intermittant bug with repeated use of this operation fixed.; 07/20/05 AL
CG PH: Longstanding bug giving low precision output fixed.; 07/14/05 AL
OP: Longstanding bug with multiple processors fixed. Accuracy of psi prompt removed.; 07/14/05 AL & PP
CE MET: New operation for maximum entropy thresholding.; 06/24/05 AL
FT: Can now link SPIDER with FFTW3 libraries by defining SP_LIBFFTW3 preprocessor variables.; 05/18/05 BR
SY DOC: New operation creates symmetry document files.; 04/07/05 JL
64 bit Opteron supported: SPIDER now can run in full 64 bit mode on Opteron systems.; 01/26/05 AL
CP FROM NIK: New operation to convert Nikon Coolscan 9000 TIFF image to SPIDER.; 01/14/05 AL
RF 3: Operation can return spatial frequency at 0.5 Fourier Shell Correlation cutoff in a register now.; 01/11/05 AL
IQ PID: New operation to obtain current process ID.; 01/03/05 AL

2004

SPIRE: SPIRE 1.2 released. Spire (SPIDER Reconstruction Engine) is a Python program providing a graphical user interface for running SPIDER procedure files.; 12/16/04 BB
CE WATER: New operation for watershed segmentation of images.; 11/19/04 AL
AP SH & AP REF: These operations no longer list 'mirrored' references in the output file. The actual projection angles are given for any mirrored projections. This may require changes in procedures which use these operations; 11/02/04 AL
PK 3R: New operation finds peaks in volume and allows a neighborhood exclusion.; 11/02/04 AL
VO EPT: New operation for rotating point/vector by an Euler angle.; 8/03/04 AL
VO IA: New operation for finding included angle between two vectors.; 8/03/04 AL
WA: New operation for warping or morphing image/volume.; 4/26/04 AL
CE VS: New operation for variance smoothing.; 3/28/04 AL
AP SH: New alignment operation replaces: APMQ, AP NQ, AP RQ, & AP RQN. Produces alignment parameter file compatible with AP REF.; 3/18/04 AL
AP REF: New alignment operation replaces: AP MD, AP RD, AP RN, & AP RNS. Produces alignment parameter file compatible with AP SH. Can optionally do shift alignment.; 3/18/04 AL
CA SRA: New operation for arbitrary coordinate image reconstitution using Coran or PCA.; 3/19/04 AL
CA SRE: New operation for Eigen-image reconstitution using Coran or PCA.; 3/19/04 AL
New document file format: SPIDER has a new document file format which handles keys > 999999 and more than 9 columns (registers). All earlier document files are still acceptable, however new document files may not work with older versions of SPIDER. (A new operation: DOC OLD will create older document file format from the newer format); 2/2/04 AL
PB CG3, PB PTS, PB RT3A, PB SH, PB IF, PB RT3, PB RT3L, & PB STP: New operations to manipulate PDB file (e.g. X-ray atomic coordinates) using same conventions as used in SPIDER. For example, 'PB CG3' calculates center of gravity of a PDB file similarly as 'CG 3' calculates center of gravity of a SPIDER file. Further, 'PB SH' will apply a shift to a PDB atomic coordinates the same way as SH will apply a shift to a SPIDER file. 'PB' commands use the same convention as SPIDER. Thus, if docking of EM SPIDER files yields shifts SX,SY,SZ these shifts can be directly applied to the original PDB file using 'PB SH'. Other 'PB' commands apply rotations and so on...; 1/22/04 PP & ZH
VM: Can output register contents in floating point.; 1/2/04 AL

2003

CA S, CA SM, CA SR, CA SRD , CA SRI, CL CLA, CL HC, CL KM, CL HE, & CL HD: CORAN, PCA & Clustering operations rewritten with modern memory management and text based output files.; 10/16/03 AL
PJ 3 & PJ 3Q: Improved anti-aliasing. For previous versions use: PJ 3 O or PJ 3Q O.; 9/18/03 PP
GP, RP: These operations now have fast access to inline files. This makes them usefull as alternatives to registers or inline document files in SPIDER procedures.; 9/8/03 AL
OR MQ, OR NQ: Order of input questions changed.; 9/5/03 AL
VM M: The 'VM' operation accepts multiple lines when invoked as 'VM M'.; 9/3/03 AL
AP MD, AP RD and AP RN: These operations can no longer create reference-rings files. Use AP I first.; 9/3/03 AL
AP RQN: Non-mirrored image checking, restricted rotation alignment operation.; 9/3/03 AL
SD IC, SD IC NEW, & SD IC COPY: New coperation to place register contents in an in-core array (document file). The array must be first declared with SD IC NEW, or by using: UD IC. The in-core array (document file) can be copied to a regular disk- based document file with: SD IC COPY; Once created an in-core arrray (document file) can be used anywhere a regular document file is used.; 7/15/03 AL
MD: Mode: 'RESULTS OFF' stops use of SPIDER RESULTS file.; Mode: 'RESULTS ON' restarts use of SPIDER RESULTS file.; 7/11/03 AL
SK: This operation can stack consecutive volumes now.; 5/29/03 AL
sigsearch.spi or (sigspub.spi & sigsloop.spi): New SPIDER procedures search for position & orientation of a small volume inside a larger volume. Use Fourier methods for calculating local correlation function (Alan Roseman, Ultramicroscopy, 2003) with a nonisotropic mask.; 3/24/03 BR
sigsearchg.spi: New SPIDER procedure searches for position & orientation of a small volume inside a larger volume. Uses real space methods for calculating local correlation function (Frangakis et al., PNAS 99 (2002) 14153-14158) with an isotropic mask.; 3/24/03 BR
PK DR: New operation for finding local peaks in image/volume with neighborhood exclusion.; 3/24/03 BR
MX: New operation for finding maximum pixels from two image/volumes.; 3/24/03 BR
HI JOINT: New operation for finding "mutual shared information" of a pair of images/volumes.; 3/24/03 AL
AD F & AD R: New convenience operations for adding/subtracting two images/volumes while applying factors. A combination of AD and AR; 3/24/03 AL
CP TO OPEND: SPIDER & Web are now able to utilize files having either byte ordering (endedness). However there is a performance penalty for reading/writing files of opposite order from your compilation specifications. Use 'CP TO OPEND' to convert files between different byte orders.; 2/28/03 AL
Header values in SPIDER files: When it is appropriate, SPIDER will transfer header positions 14-21 & 31-200 from input file to newly created output files. If there is more than one input file, e.g. in the MU operation, the header values from the first input file are used.; 2/24/03 AL
HI E: New operation for finding entropy of image/volume.; 2/4/03 AL
Indexed stacks: Indexed stacks introduced for large sparse stacks. The operation MS I must be used to create an empty indexed stack.; 1/23/03 AL

2002

OR NQ & OR MQ: New operations for alignment of two 2D images based on resampling into polar coordinates.; These operations use same method as 'OR Q' and 'OR QM'. More detailed description can be found in: Joyeux, L. and P. A. Penczek. Efficiency of 2D alignment methods. Ultramicroscopy, 92, 33-46 (2002).; 12/27/02 PP
OR Q , OR QM , OR A & OR AM: New operations for multireference 2D alignment based on self-correlation.
'OR Q' and 'OR QM' work same as 'AP NQ' and 'AP MQ' and have the same output.: 12/27/02 PP
LA & LA L: New operations add text labels to images.; 11/21/02 AL
FR G & FR F: Symbolic parameters can be nested during definition.
Also, symbolic parameters can be delimited with [] instead of < > (useful for intgrating HTML in procedure files).: 9/13/02 AL
AR SCA: New convenience operation for scaling image to a new range.; 9/10/02 AL
FR G & FR F: New operations for global text substitution in SPIDER. Also symbolic parameters can now have alphabetic labels.; 6/28/02 AL
TF SNR: New operation for CTF correction of volume series by Wiener filtering using frequency dependent SSNR; 5/7/02 JL
RF 3SN: New operation computes the Spectral Signal-to-Noise Ratio (SSNR) of a 3D reconstruction.; 5/7/02 PP
AP MS: New operation calculates translational differences with additional check of 180 degrees rotation between experimental images and a series of reference images.; 5/7/02 PP
SN RB: 5/7/02 LJ
SN RF: New operation creates a low-pass Butterworth curve.; 5/7/02 LJ
VA F: New operation computes the variance of a 3D reconstruction in Fourier space as a function of frequency.; 5/7/02 LJ
RT 3D, RT 3A, & RT 3L: These 3D rotation operations now use improved tri-quadratic interpolation.; 5/7/02 AL
RT 3DS, RT 3AS, & RT 3LS: Old operations for 3D rotation with tri-linear interpolation renamed.; 5/6/02 AL
ER WA: New operation for erosion to a watershed skeleton.; 4/25/02 AL
CE AD: New operation for contrast alteration and denoising using anisotropic diffusion.; 4/18/02 AL
CE LAH: New operation for 2D & 3D local area histogram equalization.; 4/10/02 AL
CC H: New operation for phase correlation.; 3/19/02 AL & CR
CP TO CCP4 & CP FROM CCP4: New operations convert to/from CCP4 (MRC 2000 format).; 2/23/02 AL
Eulerian angles: New documentation for SPIDER Eulerian angles.; 1/28/02 BR

2001

DOC COMBINE: New operation combines a series of document files.; 12/11/01 AL
PubSub: PubSub is now available for use at Albany for use with 'AP MQ'.; 11/16/01 AL
AP RQ: New alignment operation. Adds restricted angle search to AP MQ.; 11/08/01 HG
FF: New filter type added for "B Factor Enhancement" (contributed by Francisco Asturias).; 10/29/01 BB
JWeb: JWeb (Java Based Web) written by Bimal Rath released for Linux and Windows.; 10/25/01 BR
Perl Procedures: SPIDER procedures can be replaced with Perl/Python Scripts.; 07/31/01 AL
CP TO NT: Operation now runs on NT (and Compaq Alpha) to convert foreign byte order SPIDER files to native byte ordering.; 06/25/01 AL
DOC MINE: New operation converts SPIDER document files to a format suitable for use with SGI Mineset.; 06/07/01 AL
VO RAS: New operation rotates projection angles like VO RA but sets one of the output angles to a specified value.; 06/01/01 AL
PK M: New operation finds location of image maximum.; 06/01/01 AL
ER EDM: New operation creates an "Euclidean distance map".; 05/16/01 AL
CE FREI, CE G, CE HARALICK, CE HURST, CE LAP, CE MIN, CE MAX, CE PREWITT, CE RANGE, CE RIDGE, CE SOBEL, CE TOP, & CE VAR: New operations useful for segmenting objects in tomographic reconstructions.; 05/03/01 AL
ER SK: New operation erodes object in a binary image to a "skeleton".; 04/24/01 AL
EV: New operation allows one to set system environmental variables from SPIDER operation line.; 04/18/01 AL
Default procedure extension: The default extension for SPIDER procedures is now *.spi. Renaming avoids conflict with the standard purpose of files named *.sys on some platforms.; 03/27/01 AL
FR L: New operation allows one to set symbolic parameters locally within a procedure.; 03/19/01 AL
DI NF: New operation "dilates" (enlarges) image/volume without fusing different objects.; 03/14/01 AL
SPIDER on Parallel Clustered Systems & SPIDER on IBM SP Clusters: Techniques for using SPIDER on parallel clustered computers.; 3/13/01 AL
PA & IN: These operations now work for volumes also.; 03/01/01 AL
RT 3L: Newly documented operation rotates a volume around arbitrary line.; <02/14/01 PP
ER & DI: New operations "erode" or "dilate" a binary image/volume.; < 02/12/01 PP & AL
RM 2DN: Michael Radermacher's Radon Transform handling operations have returned to SPIDER.; 02/08/01 MR & BR
A 64-bit SGI SPIDER is now provided.: The -n32 SGI SPIDER that we provide can only address 2GB of memory. If you make reconstructions from large number of particles this may cause a memory allocation problem. We recommend use of spider5 & spider5mp on SGI R10000 & R12000 Origin & Octanes.; 01/26/01 AL
Procedures are now stored in-core.: Upon first invocation, a procedure is read into in-core memory. Further invocations of the same procedure use the stored copy. This results in substantial speed-up of reconstructions where a procedure is called for each image.; 01/23/01 AL
An operation can both read and write to the same physical stack file now.: The input and output files can both be within the same physical stack file. Note that SPIDER now may allow the user to specify the same image as both input and output file even though the results may be WRONG.; 01/23/01 AL
Can substitute environment variables into file names: System environment variables can be placed into file names by specifying ${ENV_VAR}.; 01/08/01 AL
Optional Command Line Parameters: User can now specify Results file version number and initial values for registers on the command line. This is useful in parallel clustered SPIDER runs.; 01/05/01 AL
MD: The MD "SET MEM" option is no longer used. There no longer is any restriction on how much run-time memory can be requested.; 01/04/01 AL

2000

Procedures: SPIDER procedures and "batches" no longer create a temporary file (appending 'X' to the file name) each time they are invoked.; 10/25/00 AL
PO & CC P: New operations for polar coordinates.; 10/08/00 PP
CP FROM X-PLOR: New operation to convert X-PLOR ASCII file to SPIDER format.; 09/31/00 PP
Procedures: Distinction between SPIDER procedures and batches removed. Old procedures and batches should still work.; 09/06/00 AL
SD C: Can now select which Correspondance Analysis factors are placed in the document file.; 08/22/00 AL
BP RP: An optional register on the OPERATION line receives the number of iterations completed.; 08/28/00 AL
MD: A "SET REGS" option under the "MD" operation allows the user to increase the number of registers available.; 08/14/00 AL
DOC CREATE: Continuation lines removed from document files but max. number of registers per line increased to 9.; 07/31/00 AL
EP TM: New operation for t-test versus mean.; 07/31/00 PP
RF & RF 3: Operation changed to allow use of Fourier input.; 07/17/00 AL
CP FROM ASCII: Operation changed to allow use of formatted input.; 07/14/00 AL
RF 3: Division by zero error with tiltangles other than 90 degrees using "missing wedge or cone" was fixed.; 07/10/00 PP
FT: Can now link SPIDER with FFTW (Fastest Fourier Transform in the West) libraries for Fourier Calculations.; 03/14/00 AL
CP TO XPLOR: Rotation and center of the converted map corrected.; 03/07/00 PP
SO C: New operation compares surfaces.; 03/07/00 AL
SO: New operation finds voxels at surface.; 03/07/00 AL
MU D: Order of operands for complex files corrected.; 03/03/00 PP
RT 32F: Added support for symmetries using a document file.; 01/16/00 PP

Before 2000

Source file: release.html Page updated: 14 Mar. 2008 ArDean Leith