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.

2017

New alternative SPIDER distribution download site.
You can now download the whole current Spiderweb distribution from Github.
01/25/17 AL
SPIDER source code and documentation are now available from Github as Git repositories.
There are separate repositories for: SPIDER and Spire and for Web .
01/23/17 AL & TS
Executable for Intel 64 bit architecture now created with Intel compiler.
This should improve performance on Intel Xeon CPU's.
1/20/17 AL (Requires SPIDER:***24.00...)

2016

Three Dimensional Reconstruction Protocols
There are now two alternative protocols, as used at Brno, and as used at Albany, for single particle reconstruction with different data flows and different PBS queing.
11/8/16 TS & TRS (Requires SPIDER:***23.05...)
New operation: XM S2D
Converts most XMIPP or Relion star files to SPIDER doc files.
09/29/16 AL (Requires SPIDER:***23.04...)
New operation: DOC SLICE
Puts slice from SPIDER doc file into a new doc file.
04/29/16 AL (Requires SPIDER:***23.02...)
New operation DIS
Converts SPIDER image to JPEG by invoking Imagemagick and displays the image.
04/28/16 AL (Requires SPIDER:***23.02...)
New operations: RI R & RI RV
Examine positions of rings in power spectra or CTF images. Usefull for studying electron micrographs created using phase plates.
04/19/16 Al (Requires SPIDER: ***23.01...)
New operation: CP TO STK
Convenience operation for merging a series of stacks into a single new stack.
04/18/16 Al (Requires SPIDER: ***23.01...)
New operation: FSC NEW
Simplified operation for finding FSC and resolution. Can apply a mask before calculation and reports resolution when crossing 0.5 and for 'gold standard'.
04/6/16 Al (Requires SPIDER: ***23.00...)
Suggested protocol for Three Dimensional Reconstruction improved.
Protocol, as used at Albany, for reconstruction now incorporates 'gold standard resolution' workflow and defaults to use of PBS like queing for parallel usage. Workflow has been streamlined.
3/21/16 Al & TRS (Requires SPIDER:***23.00...)

2015

Summary of transfer function operations and their recent improvements.
Operations have usage examples.
12/31/15 AL (Included with SPIDER: ***22.17...)
PJ 3F & PJ 3Q
Can create sequentially numbered output files now.
12/11/15 AL (Included with SPIDER: ***22.15...)
Web particle picking improved.
Handles particle deletion and ensures particle location pairs are complete.
9/11/15 AL (Included with SPIDER: ***22.13...)
Random Conical Tilt
Improved protocol for creating an initial reconstruction.
9/1/15 TS (Included with SPIDER:***22.13...)
CP FROM MRC
Can copy from MRC 2015 format files now. Can copy MRC stacks into SPIDER stacks.
7/15/15 AL (Requires SPIDER: ***22.12...)
Web particle picking improved.
Can start picking particles from either tilted or untilted image.
Reports current tilt when new particles picked.
6/11/15 AL (Included with SPIDER: ***22.12...)
CP TO MRC
Creates little-endian (native Intel) byte order output now.
5/5/15 AL (Requires SPIDER:*** 22.11...)
framealign.spi
New procedure for aligning raw frames from direct capture camera. Uses operation: ML
2/8/15 AL (Requires SPIDER:***22.09...)
ML
New operation uses cross correlation with multiple linear regression for aligning raw frames from direct capture camera.
2/8/15 AL (Requires SPIDER:***22.09...)

2014

FI CEN
New operation reports center of image using SPIDER's convention.
12/13/14 AL (Requires SPIDER:***22.06...)
DOC PLOT
New operation plots selected registers from a SPIDER doc file using Gnuplot.
12/10/14 AL (Requires SPIDER:***22.06...)
FS VAL
New operation finds location of minimum and maximum pixels in each row of an image and stores the info in a SPIDER doc file.
12/5/14 AL (Requires SPIDER:***22.06...)
PO R
New operation converts image to a polar coordinate representation with rays along the X dimension.
12/5/14 AL (Requires SPIDER:***22.06...)
CP FROM MRC
Can now convert 8, 16 & 32 bit MRC stacks to a SPIDER stack. Supports both unsigned and signed 16 bit input.
09/15/14 AL (Requires SPIDER:***22.04...)
FS LOC
New operation finds location of minimum and maximum pixels in image/volume.
09/16/14 AL (Requires SPIDER:***22.04...)

Maximum file name length now 160 characters.
Increased maximum file name length from 80 to 160 characters.
07/31/14 AL (Requires SPIDER:***22.00...)
SPH DECON
New operation to improve resolution of reconstructed volumes using spherical deconvolution.
05/21/14 AL (Requires SPIDER:***21.21...)
Using SPIDER with Relion data
New protocol for converting Relion star data files to SPIDER doc files
4/29/14 AL (Requires SPIDER:***21.20...)
DOC SEP
New operation separates a SPIDER doc file into multiple files based on contents of specified register.
04/3/14 AL (Requires SPIDER:***21.19...)
CP FROM TIF
New operation converts common TIFF images from EM sources to SPIDER format. (Not for compressed or color images).
03/7/14 AL (Requires SPIDER:***21.18...)
Most operations.
Most operations now come with examples linked from the manual page showing a sample invocation of the operation, sample input, sample output (images, doc files, etc.), and a link to a procedure which generated the sample output. E.g. AP SHC
2/14/14 AL

2013

Three Dimensional Reconstruction
New streamlined protocol for reconstruction without partitioning by defocus groups.
An alternative to: Reconstruction using reference projections.
11/08/13 TRS & AL (Requires SPIDER:***20.10...)
seg_img_test.spi
New SPIDER procedure windows a image then applys 25 different SPIDER filters and enhancement operations to the windowed image and places the resulting images in a stack and a montage.
8/30/13 AL
New HIS ,   & HIS R operations replace legacy image histogram operations.
Legacy HI, HI R, HI T, HI TR, HI D, HI DR,  & HI M operations are consolidated into two new operations for simplicity.
8/12/13 AL (Requires SPIDER:***21.07...)
CP TO VOL
Improved operation for stacking slices into a volume replaces legacy SK & SK R operations.
5/21/13 AL (Requires SPIDER:***21.06...)
Makefile_linux.gfort & Makefile_linux_mp.gfort makefiles available.
Makefiles for SPIDER compilation using Gnu Fortran are now provided and their SPIDER executables appear to work properly.
05/01/13 AL (Requires SPIDER:***21.05...)
MA SOFT
New operation converts SPIDER binary image to a soft edged mask.
04/25/13 AL (Requires SPIDER:***21.05...)
CP TO JPG
New operation converts SPIDER image to JPEG by invoking Imagemagick.
04/09/13 AL (Requires SPIDER:***21.03...)
SYS
New convenience operation (synonym) to replace the legacy VM operation.
3/21/13 AL (Requires SPIDER:***21.02...)
Using Relion with SPIDER data
New protocol for using Relion with SPIDER data from the Three Dimensional Reconstruction protocol.
3/15/13 AL (Requires SPIDER:***21.02...)
TF ED,   & CTF ED
The unreliable astigmatism calculations have been removed.
2/28/13 AL (Requires SPIDER:***21.02...)
Clustering and Classification Tutorial
Newly improved documentation with inlined images and modernized procedures.
2/05/13 AL (Requires SPIDER:***20.01...)
CA NOISE
New operation for creating a doc file useful for determining which CORAN/PCA factors are attributable to noise.
02/04/13 Al (Requires SPIDER:***21.01...)
CTF ED ,   TF ED ,   TF LM4 ,   & TF RCTF
These operations now accept a spherical abberation of zero.
1/12/13 GPK (Requires SPIDER:***21.01...)
OR MAP
New operation for studying rotational orientation of two images.
1/11/13 Al (Requires SPIDER:***21.00...)

2012

Random Conical Tilt
Simplified protocol for creating an initial reconstruction.
12/12/12 TS (Requires SPIDER:***21.00...)
Web displays MRC format images.
X-Window Web can now recognize and display most MRC format images and volumes.
11/29/12 AL (Distributed with SPIDER:***19.18...)
FQ   & FQ NP
Operations accept filter parameters in frequency and pixel units now.
11/29/12 GPK (Requires SPIDER:***20.18...)
ADD 2,   SUB 2,   MUL 2,   & DIV 2
New operations for pairwise addition, subtraction, multiplication, or division on a series of images.
11/02/12 Al (Requires SPIDER:***20.18...)
NORM
New operation for arithmetic normalization of image/volume using average and deviation, either overall average or average of background outside a circular mask.
09/28/12 Al (Requires SPIDER:***20.17...)
FRC & FSC
These operations can now apply a soft mask before calculating the Fourier ring/shell correlation curve.
09/11/12 Al (Requires SPIDER:***20.16...)
Three Dimensional Reconstruction protocol
Simplified procedures.
08/31/12 AL (Requires SPIDER:***20.16...)
FQ
The quick Fourier filter operation now contains options for raised cosine low-pass and high-pass filtration.
07/20/12 GPK (Requires SPIDER:***20.16...)
CTF ED
New operation determines defocus for a micrograph image.
An simpler alternative to using: TF ED on a average power spectrum.
06/26/12 AL (Requires SPIDER:***20.16...)
Particle-level CTF-correction
New protocol applies CTF-correction to windowed particle images.
An alternative to: Reconstruction using reference projections.
06/18/12 TRS (Requires SPIDER:***20.16...)
CTF FIND
New operation uses: ctffind3 to find defocus parameters.
An alternative to: TF ED.
05/18/12 AL (Requires SPIDER:***20.12...)
RO SD
New sub-operation places the one-dimensional rotational average into a SPIDER doc file.
05/16/12 AL (Requires SPIDER:***20.12...)
CP TO MRC & CP FROM MRC
Operation now convert to/from current (post 1999) MRC format input. '' This format is sometimes referred to as CCP4. Older MRC format is no longer supported.
04/16/12 AL (Requires SPIDER:***20.11...)
AP SHC AP SH, and AP REF
Added optional ability to shift/rotate experimental files using the alignment document file parameters prior to alignment. This obviates the necessity for creating a set of currently aligned images at each step during a refinement.
04/26/12 AL (Requires SPIDER:***20.10...)
BP RP 3
New sub-operation uses BP RP to create a back projection volume and two additional volumes from randomly selected half subsets of the projections.
04/01/12 AL (Requires SPIDER:***20.10...)
Methodology of 2D particle alignment documentation.
Has description of different possible methods with links to new example procedures and data sets.
3/22/12 AL (Requires SPIDER:***20.10...)
SH.
Can accept selection files or list to shift a whole series of images.
3/22/12 AL (Requires SPIDER:***20.10...)
CENT PH
New operation centers an image or series of images using method from: 'CG PH' .
3/22/12 AL (Requires SPIDER:***20.10...)
AS S
New operation averages series of images.
Can choose to create average & variance images and/or even/odd subsets of images.
3/13/12 AL (Requires SPIDER:***20.10...)
RT SF M
New sub-operation rotates, shifts, & mirrors a series of images.
Output has same size as input images.
3/06/12 AL & GPK (Requires SPIDER:***20.12...)
FRC & FSC
New operations for simple Fourier ring/shell correlation.
These operations provide defaults for unused values in RF & RF3 and directly report resolution values at common 0.5 cuttoff. .
2/22/12 AL (Requires SPIDER:***20.08...)
IQ VER
New operation:queries current version of SPIDER.
Can place version number in a register.
1/22/12 AL (Requires SPIDER:***20.07...)
MO & . MO 3
These operations can now create super-order Gaussian masks.
Super-order Gaussian masks have sharper decline at desired radius which is usually superior to using normal Gaussian (soft) masks.
1/14/12 GPK (Requires SPIDER:***20.06...)
BP CG & BP CG 3
These operations can now use FBS interpolation.
These operations have option of using slower FBS interpolation to create a higher resolution output volume.
01/06/12 AL (Requires SPIDER:***20.06...)
Use of NSAM, NROW, & NSLICE.
SPIDER image dimensions are now referred to as: NX, NY, & NZ instead of: NSAM, NROW, & NSLICE. This makes SPIDER conventions similar to those used by MRC, XMIPP, and SPARX.
1/6/12 AL (Requires SPIDER:***20.06...)

2011

CL CLA.
Can now create a dendrogram of any desired factors and omit certain factors.
11/30/11 AL (Requires SPIDER:***20.04...)
AP SHC.
Can now restrict the inplane rotation search range.
11/11/11 AL (Requires SPIDER:***20.03...)
ROT
New operation for rotating images/volumes.
This operation has improved interpolation and corner value options.
Replaces 'RT', 'RT M', 'RT B', 'RT 3', 'RT 3D', and 'RT 3DS'. Which will be removed in the future.
10/4/11 AL (Requires SPIDER:***20.00...)
ROT A
New operation for rotating images/volumes around an abitrary point.
This operation has improved interpolation and corner value options.
Replaces 'RT C', 'RT 3A', and 'RT 3AS'. Which will be removed in the future.
10/4/11 AL (Requires SPIDER:***20.00...)
ROT L
New operation for rotating volume around a line
This operation has improved interpolation and corner value options.
Replaces 'RT #L' and 'RT 3LS'. Which will be removed in the future.
10/4/11 AL (Requires SPIDER:***20.00...)
Web installation on Gnome & OSX.
New executables for X-Window Web now offer full functionality on Gnome and OSX including contrast adjustment and no colormap flashing. Simple installation also.
9/14/11 AL (Distributed with SPIDER:***20.00...)
IP FS.
New algorithm for resizing images/volumes gives improved interpolation results compared with 'IP'.
09/4/11 GPK (Requires SPIDER:***20.00...)
New procedure restack.spi for renumbering image stacks.
Can restack SPIDER images listed in a set of image selection doc. files. Can decrease or increase the number of stacks and remove unused images. Creates new stacks and new selection doc files./
8/04/11 AL (In SPIDER:***19.11...)
Image header, FI H, and ST H
Have new fields (locations) in the file headers for storing a project number, micrograph number, and image number. This improves interoperability with Xmippp.
8/04/11 AL (Requires SPIDER:***19.11...)
Web for X-Window use.
X-Window Web now has reduced colormap flashing and better color handling. Several operations including Tilted pair particle selection have been improved. Has new widgets in main menu bar.
8/04/11 AL (Distributed with SPIDER:***19.11...)
Web installation simplified.
X-Window Web installation is now simpler. Web is now statically linked with Motif libraries so these libraries are no longer needed on your machine. Web for 8 bit deep visuals has been retired.
8/04/11 AL (Distributed with SPIDER:***19.11...)
CC H.
Legacy phase cross correlation operation recovered.
08/4/11 AL (Requires SPIDER:***19.11...)
RT SF.
New algorithm for rotating and shifting images gives improved interpolation results compared with 'RT SQ'.
08/4/11 GPK (Requires SPIDER:***19.11...)
AP SHC.
Faster version.
03/14/11 AL (Requires SPIDER:***19.05...)
DN MS
New operation for denoising images using 'mean shift'. (Requires SPIDER:***19.05...)
03/10/11 GK
XM MA
New operation to create an Xmipp selection file from a SPIDER selection doc. file. (Requires SPIDER:***19.02...)
01/26/11 AL
BP CG 3
New operation uses BP CG to create a back projection volume and two additional volumes from randomly selected half subsets of the projections. (Requires SPIDER:***19.01...)
01/06/11 AL

2010

MD
Mode: '() OFF' is now default.
Users no longer need to surround numerical input in procedures with ()'s when inside a do-loop. (This overcomes the most common problem users encounter when using SPIDER).
12/20/10 AL (Requires SPIDER:***19.00...)
ST H
New convenience operation to set file variables in the file header by name (not by location in header).
11/26/10 AL (Requires SPIDER:***18.20...)
DOC STAT.
New operation to find statistics for a document file column.
11/23/10 AL (Requires SPIDER:***18.20...)
TF COR.
New convenience operation for faster CTF correction.
11/03/10 AL (Requires SPIDER:***18.19...)
DOC SORT.
Does either ascending or descending sorts now.
10/26/10 AL (Requires SPIDER:***18.19...)
MS.
Handles inline stacks larger than 2.1 Mb now.
10/20/10 AL (Requires SPIDER:***18.19...)
AP TOOL.
New operation that helps to select shift area, shift steps, and ring step parameters for use in AP SH.
10/14/10 AL (Requires SPIDER:***18.18...)
Sample procedures for reconstruction using reference projections no longer center group volumes.
Improved procedures give increased resolution.
9/14/10 AL (Requires SPIDER:***18.18...)
SD.
Comment keys can have keys -9999999 .. -1. Also by using '//', a comment line containing substituted variables can be placed in a document file.
8/31/10 AL (Requires SPIDER:***18.16...)
publish.
When using PubSub for controlling a cluster, publish can now be done remotely. This allows the master SPIDER job to run on a different server from the PubSub master.
8/4/10 AL (In SPIDER:***18.16...)
subscribe.
When using PubSub for controlling a cluster, subscribe no longer blocks when a node encounters NFS communication problems.
8/4/10 AL (In SPIDER:***18.16...)
IQ SYNC D.
New operation that waits for existence of a file then deletes it.
08/4/10 AL (Requires SPIDER:***18.15...)
AP SHC.
Faster version of: AP SH
07/14/10 AL (Requires SPIDER:***18.14...)
AP SCC.
Added ability to restrict image search to X axis or Y axis only.
02/26/10 AL (Requires SPIDER:***18.09...)
AP SH.
Added optional input for specifying different X and Y shift search ranges.
02/26/10 AL (Requires SPIDER:***18.09...)
Sample procedures for reconstruction using reference projections simplified.
Procedures have been simplified for easier use and increased speed.
1/18/10 AL (Requires SPIDER:***18.08...)
New procedure nat2stk.spi for use with data from Nature Protocols paper.
Procedure converts data set to use SPIDER stacks and most recent procedures for reconstruction using reference projections.
1/17/10 AL (In SPIDER:***18.08...)

2009

IQ DIR
New operation to query existence of a directory.
12/28/09 AL
@@procedure
New operation for invoking a procedure without a new namespace.
Same as @procedure, except that local numerical and string variables defined/set in the procedure are visible in the calling procedure.
11/31/09 AL
New syntax for creating string (symbolic) variables
Replaces FR L, FR G, FR LS, & FR GS
SPIRE supports this syntax in SPIDER release: ***18.14.
7/31/09 AL
New syntax for creating global register (numerical) variables
Replaces RR G
SPIRE supports this syntax in SPIDER release: ***18.14.
7/31/09 AL
CL CLA, CL HC
Operations rewritten (have slightly different inputs) to improve dendrogram plots and allow determining which images/elements are assigned to a class/cluster using CL HE and CL HD
6/11/09 AL
CL HE, CL HD
Operations rewritten (have slightly different inputs) in conjunction with changes to CL CLA and CL HC. It is now easy to determine which images/elements are assigned to a class/cluster
6/11/09 AL
UD MAX
New operation to find highest/lowest value in specified column of a document file.
5/28/09 AL
FI H
New convenience operation to retrieve file variables from the file header by name (not by location in header).
5/15/09 AL
MO 3
Added option which creates a Gaussian soft mask volume.
4/22/09 AL
Mac OS X executables available
OS X SPIDER and Web executables are now available in the current release.
4/9/09 AL
Read SPIDER files into Matlab.
Matlab scripts (M-files) are now available for reading/writing SPIDER files directly into Matlab data types for processing and visualization. The files are available from the Matlab file exchange: www.mathworks.com/matlabcentral/fileexchange .
2/6/09 BB

2008

New SPIDER usage protocols
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols 3, 1941-1974 (2008)
Download tar archives of procedures.
12/20/08 TRS
Simplified Spire installation.
Version 1.5.3 of Spire has a greatly simplified installation. It now comes with its own Python and all the prerequisite Python libraries needed to run Spire and the associated graphical tools.
11/25/08 BB
SPIDER Linux OMP executables.
Use of new compiler release allows SPIDER Linux OMP excutables to run more than four concurrent OMP processes.
10/30/08 AL
Simplifying SPIDER use under MPI.
When starting SPIDER under MPI with 'mpirun', a '--' at end of SPIDER's command line arguments allows SPIDER to ignore any arguments appended by 'mpirun'.
10/25/08 AL
AP REF, AP SH, BP 3F, BP 32F, BP CG, & BP RP.
Operations updated to improve use under MPI.
10/25/08 AL
LO I, LO LSD, & LO.
New operations to speed up RAMOS motif signature search.
8/05/08 AL
Particle verification
New documentation derived from: "Particle verification for single-particle, reference-based reconstruction using multivariate data analysis and classification," by Shaikh, Trujillo, LeBarron, Baxter, and Frank, Journal of Structural Biology 161: 41-48 (2008).
7/02/08 TRS
AP SH
Added method to restrict rotational alignment search by limiting the 'rays' searched.
6/23/08 AL
AP C
Merged rotational alignment and classification operation replaces: AP CA, AP CM.
6/18/08 AL
OR SH
Merged single image rotational and shift alignment operation replaces: OR MQ, OR NQ.
6/09/08 AL
OR R
Merged single image rotational alignment operation replaces: OR 2, OR 2M.
6/09/08 AL
UD FIND
New operation to retrieve a line from a document file which has a specified value in a specified column.
6/04/08 AL
Irix Support Discontinued
Starting with release 16.* we no longer provide executables for use with SGI Irix or SGI Linux.
5/23/08 AL
AP SH
Speed increased by using FFTW3 in Fourier steps and better data flow.
5/19/08 AL
AP REF
Speed doubled by using precalculation of trigonometric values, FFTW3 in Fourier steps, and better data flow.
5/19/08 AL
BP 3G
New operation for back projection using non-uniform Fourier transforms ('gridding').
5/19/08 AL
PJ 3G
New operation for projection using non-uniform Fourier transforms ('gridding').
5/19/08 AL
AP SCC
New operation rapidly calculates translational differences between experimental image/volume(s) and a series of reference image/volumes(s). Pads images before cross correlation in Fourier space.
5/19/08 AL

2007

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 Mok 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

2006

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 (String) Variables
Symbolic variables 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 useful 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. Uses 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 is 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
Before 2003

Source file: release.html     Page updated: 25 Jan 2017     ArDean Leith
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