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.
- New operation: IQ VER
queries current version of SPIDER.
- Can place version number in a register.
- 1/22/12 AL (Requires SPIDER:***20.07...)
- New operation: CG SYM
gives improved determination of 'center' of an object in a
noisy image.
- Better center location than: 'CG', or
'CG PH'
for noisy images.
- 1/22/12 GPK (Requires SPIDER:***20.07...)
- Operations: MO &
. MO 3
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...)
- Operations BP CG &
BP CG 3
can 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...)
- CL CLA.
- Can now create a dendrogram of any desired factors and omit
certain factors.
- 11/30/11 AGL (Requires SPIDER:***20.04...)
- AP SHC.
- Can now restrict the inplane rotation search range.
- 11/11/11 AL (Requires SPIDER:***20.03...)
- New operation: ROT 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...)
- New operation: ROT A 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...)
- New operation: ROT L 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
- 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...)
- 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
- 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 TS
- 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
(in press).
- 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
- 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
- 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
- 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
- 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. 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
- Before 2003
Source file: release.html
Page updated: 23 Jan. 2012
ArDean Leith
©
Copyright Notice /
Enquiries: spider@wadsworth.org