Changes marked with ** are particularly noteworthy, ones marked with * may also be of interest to typical users.
** 9/20/07: Added ctfplotter for determining defocus in groups of low-dose tilt images, and ctfphaseflip to correct for CTF in tilted images with phase flipping only.
** 7/19/07: Added sirtsetup to set up command files for SIRT.
** 2/19/07: Tiltalign modified to solve for a beam tilt angle (non-perpendicularity of beam and tilt axis) and to express it as tilts around the X axis and modifications of tilt angle and rotation, so that this can be incorporated into the reconstruction. Added an option to specify the size of local areas instead of the number, in which case local areas will cover the area occupied by fiducials instead of the image area. Made local fits skip views with no points and make groups larger when views have fewer than 3 points.
* 12/12/07: Made Solvematch compute the scaling along each of the three axes and issue a warning if the scaling is not isotropic within 10%.
* 12/6/07: Made Tilt able to produce origin values that are based on the aligned stack origin and account for all size and shift entries so different volumes will be congruent.
* 10/12/07: Changed interpolation routines used by Newstack and Blendmont to operate around the true center of the image instead of being offset by half a pixel. This will change some output, but now the tilt axis should be located properly for aligned tilt series rotated by large angles like 90 degrees.
* 9/24/07: Copytomocoms now sets up a SCALE entry in tilt.com that roughly compensates for the dependence of Tilt's scaling on the width of the input data.
* 7/16/07: Added Densnorm for density (mass) normalization.
* 7/16/07: Tilt can now reproject from a tomogram file and produce reprojections that match the input data even when X axis tilting, Z factors, or local alignments were used. It can take weighting factors for a relative mass normalization.
1/10/08: Fixed Ccderaser to scale the model file to pixel coordinates on the current stack even if the model came from a binned stack.
12/27/07: Added an option to extracttilts to give a warning if the tilt angles are suspicious; made copytomocoms use the option.
12/11/07: Removed warning from Tiltalign when solving for a single X tilt variable plus rotation.
10/19/07: Fixed defocus scaling bugs in ctfplotter and ctfphaseflip.
10/10/07: Fixed Corrsearch3d's handling of volume shifts when volume sizes are unequal.
10/4/07: Made Corrsearch3d compute positions and correlation coefficients more carefully to avoid numeric problems correlating solid gray areas.
10/1/07: Handling of defocus values in multiple tilt ranges improved in Ctfphaseflip; documentation of defocus file fixed.
10/1/07: Fixed bug in filter setup function that would crash Tiltxcorr if run with no filtering (broken in 3.10.10).
9/11/07: Added options to sirtsetup for better management of intermediate reconstructions, and added more instructions to man page.
9/8/07: Fixed Tilt's reading of SHIFT and some other options, broken in PIP upgrade, 3.10.13.
8/17/07: Fixed sirtsetup to work with binning and when making a log stack.
8/10/07: Sirtsetup has a man page and can work with a tilt command file that has a LOG entry.
8/10/07: Densnorm has new options to handle data stored as signed integers with 32768 subtracted.
7/16/07: A small zero-frequency component was added to the backprojection in Tilt to prevent some artifacts from lines having different mean levels.
7/16/07: Splittilt modified to handle reprojections from a tomogram and to be compatible with setting up files for iterative operations.
6/21/07: Converted Tilt to PIP input without having to retain old code by torturing PIP into accepting a few odd things.
5/18/07: Added option to Extracttilts to extract dose information saved by SerialEM.
5/3/07: In Tiltalign, changed projection stretch to be after rotation so a beam tilt can be used correctly, discovered a variable redundancy in the projection stretch and reduced it to a projection skew of X and Y axes.
3/19/07: Changed the way Solvematch determines the center shift so it won't get screwed up if the center points are all on one surface.
3/8/07: Made Tiltalign put out at least two local areas in each direction and made Tilt insist on this.
3/8/07: Compacted output from beam tilt search, and fixed output and alignlog so it does not show up in error output from alignlog, but in a new -b output.
3/5/07: Renamed option in Tiltalign to FixedOrInitialBeamTilt.
Changes in eTomo
** 11/12/07: Interface to anisotropic diffusion added to eTomo.
** 2/9/07: Etomo has a new interface for refining the alignment of joined tomograms.
* 9/28/07: Etomo now supports parallel processing on a cluster defined in cpu.adoc, and queuechunk is fixed to work better on a PBS queue.
* 8/28/07: In eTomo parallel processing allowing Resume after exiting and re-starting eTomo.
* 8/16/07: In eTomo, added ability to set the size of the aligned stack in the advanced section of the Newstack/Blendmont panel. This is to allow the SIRT procedure to be used on a trial subarea, and to allow oversized recontructions to recover area lost due to rotation of the tilt axis to vertical.
* 8/8/07: Added Default values to the Settings dialog so that the user can customize the initial value of some fields on the Setup and Post Processing dialogs.
* 7/27/07: Clarified the etomo fiducial tracking interface. Instead of a separate button to copy the fiducial model to the seed model, there is now a button to copy and then track the resulting seed model.
* 5/29/07: Improved error reporting for load averages. Added a "Restart Load" button which causes Etomo to restart any failed load averages.
* 3/8/07: Etomo added a tiltalign parameter to the Fine Alignment dialog, TargetPatchSizeXandY, which can be used in preference to NumberOfLocalPatchesXandY.
* 3/7/07: Etomo: Added beam tilt fields to the Fine Alignment dialog. The .xtilt file will be created by align.com and will be use by tilt.com.
12/17/07: Nicing processchunks when using a queue.
12/12/07: Automatically running newstack, blendmont, and tilt with AdjustOrigin. For a single axis tomogram created prior to this change, trimvol will be run the option "-k" which prevents the origin adjustment.
12/10/07: Processchunks Resume will work after exiting and rerunning eTomo even if eTomo exits abnormally. Resume will not work if processchunks is still running.
8/21/07: In eTomo added a warning message to Tomogram Combination for situations where the X and Y min and max values should be changed.
7/30/07: In eTomo Join, allowing the project to be saved before "Make Samples" is pressed.
7/27/07: In eTomo Tomogram Combination the "Starting points to use from A" field can now take "/", which it will convert to an empty string.
5/22/07: In the Etomo Parallel Processing table, added the ability to exclude rows based on the current user. See "users" in the cpuadoc man page.
5/21/07: In the Etomo Parallel Processing table, added the ability to exclude rows based on the type of interface in use (Join, PEET, etc). See "exclude-interface" in the cpuadoc man page.
5/21/07: In the Etomo Parallel Processing table, removed the Users column, which is inaccurate in Fedora Core 6. To keep the Users column, add a "users-column" attribute to the global section of cpu.adoc.
5/18/07: In Etomo Parallel Processing, the lowest possible Nice is now 4. This can be changed by adding the attribute "min.nice" to the global section of the cpu.adoc file.
4/23/07: In Etomo Rejoin, fixed the upper slice limit sent to Finishjoin for the final rejoin.
2/22/07: Fixed a problem in Etomo - Parallel Processing that may have affected some bash users with .cshrc files. The local load average was always failing.
PEET Interface in eTomo
** 5/3/07: Etomo now includes an interface for the PEET particle averaging
programs.
12/17/07: Modified PEET interface to handle a change in a flag definition in PEET.
7/25/07: In eTomo PEET added the ability to read the tilt log file to retrieve a tilt range.
7/23/07: In eTomo PEET screens, fixed button to bring up averages, and changed sense of the checkboxes to take reference or average equally from all tomograms to match code.
6/7/07: In Etomo - PEET, allowed the root name to be changed when importing a .prm file.
6/7/07: In Etomo - PEET, allowed nonsupported parameters in the .prm file.
6/6/07: In Etomo - PEET, added "Change Model" button to the Volume Table.
6/5/07: In Etomo - PEET, added flgWedgeWeight to the interface ("Use tilt range in alignment").
6/5/07: In Etomo - PEET, fixed a bug which prevented the "New PEET" menu item from being enabled correctly.
6/4/07: In Etomo - PEET, added "Copy Parameters" button, which allows the reuse of a preferred set of parameters.
5/31/07: In Etomo - PEET, fixed a problem creating the .epe file when importing a .prm file or duplicating a project.
5/18/07: Etomo PEET interface now includes row deletion, importing from an existing prm file, and data set duplication.
Changes in 3dmod
** 8/13/07: Added a Locator window to 3dmod to keep track of and manipulate the
area displayed in the Zap window.
** 7/13/07: The Xyz window now has fixed subwindows for each area in which the images zoom up and pan around. Keypad insert key works for modeling here.
** 6/15/07: In Slicer, the volume can now be rotated relative to its current orientation with mouse or keypad keys just like the model in Model view. This is done with Shift key down, or with a new Shift lock toolbar button on. Also fixed various synchronization problems with the slicer angle dialog plus two bad but obscure bugs.
** 5/29/07: Slicer has a new mode in which the center point is not tied to the current image/model point and the mouse now pans the image; there is a toolbar button to switch between this and classic mode. A slicer can now be time locked too. Automatic scaling is used to match the image contrast to that of a singel slice when 4 or more slices are being summed. FFT's are also automatically scaled to have contrast in the same range as images. Images edges are now tapered before taking an FFT to eliminate artifacts.
** 5/24/07: Added a dialog to 3dmod to save slicer angles in the model and reset slicer to the saved angles.
* 1/19/08: Added an On button to the Draw Data Type in model view object edit to turn objects back on without having to select Contour/Mesh.
* 1/8/08: Fixed contour sort routine and made it work from 3D distances.
* 11/30/07: Added ability to link model view to top slicer and rotate them together.
* 10/16/07: Added ability to make the side views bigger or smaller relative to the XY view in the XYZ window, and added a centering button.
* 11/13/07: Added setting in 3dmod preferences to control the volume size at which slicer speeds up its computations, made it drop high-resolution display before radically reducing number of slices averaged, gave credit for multiple processors if defined by IMOD_PROCESSORS, and eliminated double draws when changing slicer angles.
* 11/9/07: Added ability to set a directory to receive snapshots in 3dmod.
* 9/21/07: Added option to show stored values with constant color to make it possible to distinguish ones below and just above a threshold.
* 9/20/07: Added ability to visualize the current clipping plane as a semitransparent plane and improved predictability of clipping planes by making them rotate around the point closest to the center of the window.
* 9/17/07: Added environment variable IMOD_RETAIN_FSCACHE to keep 3dmod from dismissing data in file system cache while loading it (see man imodenv).
* 8/6/07: Added #/$ hot keys to start/stop movies in Z in place of mouse click.
* 7/19/07: Added 3dmod hot keys !/@ for jumping to first and last time index, or to start and end limits on Time set in the Edit-Movies dialog.
* 7/8/07: 3dmod changes to make bulk model cleanup operations easier: Object deletion will delete multiple selected objects. There is an Object Combine menu entry that will move all contours from multiple selected objects into one object and delete the other objects. Popup messages asking for confirmation of high-level deletion operations now have a Yes Always option. Groups of objects can be switched between open and closed and the automatic new contour feature can be selected with buttons in the Lines panel of the Model View Object Edit dialog. Dragging the mouse in model view with the third button and the Ctrl key down will add contours that are crossed to the selected contours.
* 6/7/07: Added Ctrl-Shift-D hot key to delete a surface, and added an option to Object-Type window to get a new contour automatically on each new section when modeling with open contours.
* 5/31/07: Added a time toolbar to Slicer identical to the one in the Zap window, and added an angle-saving toolbar that appears when the Slicer Angles dialog is opened and has some of the controls that were in the Slicer Angle dialog.
* 4/6/07: Increased range of light movement in model view and made rate of movement fairly uniform across range of angles.
1/21/08: Synchronized model view object edit and object list after object deletion, renumbering, and combining.
1/19/08: 3dmod creates a new empty object after the user deletes all objects to avoid crashes.
1/13/08: Fixed some problems with Zap window cursor with multiple windows.
12/12/07: Fixed panning in Xyz window from getting stuck at one end.
12/6/07: Allowed 3dmod to sort contours in open contour objects.
12/4/07: Changed 3dmod to support cursor-like extra object drawn by plugin, and implemented array of extra objects to avoid conflicts between components using them. Documented 3dmod functions available to plugins, exported undo/redo and selection list functions, and modified beadfixer2 to serve as better example.
11/10/07: Made s save model in slicer window, assigned l hot key to show slice instead. Fixed updating of slicer angle window when new model is created, and stopped synchronization to slicer angle table when Auto button is turned on since direction of action is ambiguous.
9/16/07: Switched high resolution drawing in 3dmod from quadratic to cubic interpolation, which gives less pixelation at high zoom amd is only 15% slower.
8/15/07: Fixed bug in slicer that crashed 3dmod, which showed up with new mouse rotations.
8/7/07: Fixed picking of points in model view to avoid context-setting error messages.
6/18/07: Fixed model view rotation around X axis.
6/13/07: Added ability for 3dmod to read PIF files produced by Bsoft.
6/6/07: Fixed miscentering in Zap window after doing a drag draw, and after deleting points, by setting current point coordinates correctly.
6/4/07: Attaching to a model point in Slicer now rotates points for analysis so that it will pick points only within 0.5 pixel of the current plane.
5/29/07: The Zap info button now reports a trimvol command for excising the selected area of the current slice that takes account of whether the data are loaded in flipped and is easily extensible to multiple slices.
5/5/07: Movie snapshots from Zap or Slicer will no longer check for the first free snapshot filename, which gets slow with many hundreds of files.
4/26/07: Made 3dmod set model image reference information correctly when the image is a mirrored FFT, so model will display interchangeably between mirrored and non-mirrored FFT.
3/28/07: Fixed crashes of 3dmod when focus is in a toolbar edit box in slicer, zap, graph or tumbler window and window is closed with Escape.
3/9/07: Made Zap montage snapshots work when taking automatic movie snapshots.
Changes in General Processing Programs or Infrastructure
** 4/26/07: Rebuilt imodmop to incorporate ability to make a projection series
(formerly done by imodcmopp), handle all kinds of data including FFT's,
allow control of output image size and image scaling, extract regions
defined by scattered points and cylinders along open contours, and output
either monochrome or color data.
** 4/8/07: Added programs Edgepatches, Stitchalign, and Tomostitch for stitching together adjacent tomograms.
* 1/8/08: Edpiecepoint can now be used to generate a piece list for a montage.
* 12/6/07: Added option to Blendmont to adjust origin for starting X, Y, Z.
* 12/5/07: Converted Boxstartend for extracting subvolumes at model points to PIP input and made it able to output practically any size volume.
* 12/5/07: Added option to Newstack to adjust origin values for scaling, binning, and outputting a subarea of the original volume, and made Trimvol use this option, so that models built on a volume will display correctly on a subvolume.
* 11/27/07: Added option to imodmop to extract just volume needed for objects being painted.
* 11/22/07: Generalized the kernel smoothing in 3dmod and clip to use Gaussian kernels, 3x3, 5x5, or 7x7, with specified sigma. Using a larger sigma should reduce need to iterate, but also added an option to iterate smoothing in clip.
* 10/21/07: Converted Boxavg to PIP input, made it take a model file instead of a point file, and made it operate with and align to non-integer coordinates.
* 10/18/07: Added Point2model as a complementary program to Model2point to allow simple format for getting data into and out of IMOD models.
* 10/15/07: Fixed Tif2mrc when reading unequally sized images on Windows, added an option to set output size, made different sizes work with all data modes and made the image be centered in the output area when it is clipped or padded.
* 10/3/07: Made Taperoutvol set the origin to match the coordinate system of the input volume, and made Assemblevol set the origin based on the origin of the first input subvolume. Thus origins should be preserved through chunk processing and reassembly.
* 9/16/07: Enhanced install scripts to provide options for specifying the destination to copy startup scripts to or skipping this step, added help output, fixed handling of relative path for install location.
* 9/14/07: Added script by which Processchunks can put jobs on a cluster queue.
* 9/12/07: Added options to model2point for getting non-integer output, and object and contour numbers.
* 9/11/07: Added an option to trimvol to allow scaling of floating point to integer.
* 6/11/07: Upgraded ascii model format to retain more properties.
* 5/31/07: Added options to Mtffilter so that it provides the same set of filter shapes as Enhance does, and can be used in place of Enhance.
* 5/25/07: Added ssh options to both etomo and processchunks to keep ssh from asking for passwords when there is either no account or no passwordless access. Processchunks also turns off strict host key checking.
* 5/18/07: Added options to imodmop to specify background fill value and color.
* 1/31/07: Added option to Xfmodel to specify a scaling of the shifts so it can transform a model built on binned stack with transforms for unbinned stack.
* 12/20/06: Added options to Newstack for outputting sections at a regular increment and for outputting blank sections given section numbers out of range. Finishjoin now has an option to accept numbers out of range for producing blank slices between sections.
1/9/08: Fixed error from closing file twice with clip splitrgb.
12/13/07: Provided renamed executables and script wrappers for patch2imod and imod2patch since Vista decided they were dangerous.
12/10/07: Fixed processchunks failure when it read a long error message from nad_eed_3d, improved argument processing in nad_eed_3d to detect missing values after options.
12/10/07: Fixed problem with vmstocsh created 11/20/07, that makes scripts fail with FC2 package.
12/6/07: Fixed Newstack min/max values in output header when not rescaling.
12/4/07: Changed Linux startup scripts to place IMOD/bin on path only once.
11/20/07: Switched to using individual script for each Fortran graphics program (nda, mtk, etc) in the Mac so they can run from command files without using runimodqtapp; added commands to put qtlib on the library path to scripts produced by vmstocsh and vmstopy.
11/17/07: Increased allowed length of concatenated and temporary file names in Fortran programs from 80 to 320; increased filename lengths to 320 for rotatevol, matchvol, warpvol and newstack.
11/13/07: Fixed linklibs-mac to work on OS X 10.5, to include new IMOD library, and to provide more error checks.
11/9/07: Added option to imodmesh to recompute normals from an existing mesh.
11/1/07: Fixed reading of ascii model with DOS line endings
10/29/07: Converted Xcorr to PIP input, removed redundant filters, adjusted origin when run on a subset of stack, renamed to Xcorrstack to reduce confusion with xcorr.com.
10/24/07: Fixed install script to work on Vista and allowed alternate installation directory for Windows.
10/19/07: Fixed two bugs in mtk: computation of multiple graphs (broken 1/5/06) and selection of neighboring mesh objects with multiple graphs. Also added an option to get lengths of connector lines between points of close approach.
10/14/07: Fixed model2point to output index coordinates by default and added an option to get scaled model coordinates instead.
10/14/07: Changed file size shown when opening a file to be in KB instead of 512-byte blocks and labeled with a K.
10/3/07: Made Processchunks able to run without a -finish.com file.
10/3/07: Made nad_eed_3d work with unsigned integer (mode 6) input.
10/1/07: Added test mode output to Edgepatches.
9/20/07: Split libimod into pure model library and a utility library.
9/7/07: Fixed Blendmont to stop truncating integer input data at 0 for mode 1 or 32767 for mode 6.
8/30/07: Fixed Rotatevol, Matchvol, Warpvol to work with more than 32767 slices in a layer of cubes.
8/30/07: Made clip flipyz/rotx read multiple slices of data up to 500 MB worth then write the slices out, reducing real time consumed by 6-10 fold.
8/20/07: Fixed Findcontrast to work with densities over 1000000.
8/15/07: Fixed processchunks to work with > 999 chunks, up to 9999.
7/18/07: Fixed some problems with edgepatches run with narrow overlap zones.
7/15/07: Added ability to enter 0,0 as limits to assemblevol when there is no overlap between volumes being assembled.
7/15/07: Fixed filling of edge areas when using xyzproj with constant scaling.
6/27/07: Increased point limit in solvematch to 10000.
6/7/07: Improved error reports from low-level I/O routines for Fortran to include filename and to report a system error string correctly.
5/22/07: Fixed bug in Blendmont (added in 3.10.5) that gave bad origin values.
5/22/07: Changed Extracttilts after changing the way that SerialEM packs a float into two shorts in the extended header.
5/7/07: For 32-bit Windows, added flag to 3dmod and midas to allow them to access up to 3 GB of memory instead of 2 GB, if boot parameter /3GB is used.
5/3/07: Fixed bugs in Processchunks when there are failures running a sync file or running a command on a machine.
4/26/07: Added option to Xyzproj to keep the scaling constant at different tilt angles, instead of dividing by number of pixels along a projection ray.
4/11/07: Added option to Imod2vrml to output separate point/normal list for every polygon (an attempt to avoid holes in some viewers.)
4/9/07: Added option to Blendmont to make it exclude gray fill areas from edge function analysis.
4/7/07: Increased array limits in Warpvol and Findwarp to support work with supermontages.
4/7/07: Added options to Blendmont to support running in parallel.
4/7/07: Added options to Blendmont to specify range in Z over which an edge gives good edge functions, to eliminate effects of bad edge functions when stitching adjacent tomograms.
3/28/07: Fixed bug in binvol for (large?) images with ny < nx.
2/12/07: Changed Newstack to provide better fractional pixel origin values when data are binned and the output size is a specified size.
2/2/07: Fixed bug in binvol when specifying input file with -input.
1/31/07: Stopped Finishjoin from scaling offset down by binning.
1/31/07: Added option to rotatevol to set fill value for areas with no image.
1/31/07: Made clip transfer header "start" information to output file.
1/24/07: Finishjoin no longer allows dashes in the slice range entries, because negative numbers can now be entered to get gray slices.
1/23/07: Made Blendmont bin overlap areas for cross-correlation when they exceed 1Mpixel in size.
1/6/07: Made Mtk preserve point sizes when assigning contours to new objects.