MIPAV change list 2.x

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2.7 (06/23/2006)

  • File handling
    • When saving from MINC to DICOM, the minc header is checked for a DICOM-converted intance number tag (0020,0013), and that number is used as the base instance number for each slice of the new DICOM image.
    • Fixed the DICOM browser tag selector dialog column sizing on some Linux systems.
    • All file open/save progress bars now respect the -hide command line option.
  • Algorithms
    • Fixed bugs in Subsample, Transform, Direct resample, IHN3 correction, and Transcode algorithms.
    • Allow two types of vector filtering instead of just one for Median and Mean filter algorithms of color images.
    • The interface used to indicate whether an algorithm should be run in a new thread has been changed slightly (this may break some Plugins, requiring them to be changed and recompiled).
  • Utilities
    • Paint to Mask conversion fixed for color images.
  • VOIs
    • Fixed VOI properties and VOI statistics calculation and tabbing of center of gravity data.
    • Fixed VOI statistics calculation of center of mass for the first rectangle VOI contour in an image.
    • The user can now select the number of digits to calculate to after the decimal point and whether to force the display of trailing zeros in the VOI properties and VOI statistics dialogs.
    • Fixed VOI select-all operation.
    • Fixed a bug in the execution of MaskToVOI script actions with large VOIs.
  • Miscellaneous
    • Two bugs in the creation and resizing of image frames on Linux systems have been fixed. These bugs caused MIPAV to intermittently freeze when new images were created by algorithms on some systems.

2.6 (06/09/2006)

  • File handling
    • Refactored and improved consistency of image origin determination for all file types.
    • MINC
      • Saving DICOM to MINC now exports all non-array (value multiplicity) DICOM tags to the MINC header.
    • DICOM
      • Saving to DICOM from MINC now exports all DICOM-style tags in the MINC header (a partial set of tags was being exported previously). Tags the user wants to export must be in the MIPAV DICOM dictionary(dicom_dictionary.txt in the MIPAV install directory).
      • Fixed calculation of slope and intercept when saving from MINC to DICOM.
      • When saving to DICOM from another format, the DICOM tag dialog is skipped if a script is being executed.
      • When saving to DICOM from another format, "(0020,0032) Patient position" and "(0020,1041) Slice location (patient)" are now generated for each DICOM slice.
      • DICOM receiver now handles DICOM images with implicit/explicit group two tags.
    • Interfile
      • Support for more image information has been added.
    • NIfTI
      • Fixed sign errors when reading and writing the header.
    • Analyze
      • The user can now decide to always save .img files in Analyze format in the MIPAV options dialog.
  • Algorithms
    • Color edge has been added to the list of available spatial filters.
    • Added density-based clustering algorithm.
    • Blind deconvolution
      • Fixed blind deconvolution for 2D grayscale and color images.
      • Added 3D blind deconvolution for grayscale and color images.
      • Added optional microscope-based constraints to blind deconvolution.
    • Option added to do vector median filtering of color images.
    • Option added to do vector mean filtering of color images.
    • Added cell-tracking to the active gradient vector flow boundary algorithm.
    • Fixed a bug in the fill holes 3D morphology operation.
  • Utilities
    • Added the ability to rotate an image about the X, Y, and Z axes by 180 degrees.
    • Added the ability to create a 3D or 4D mask for image B of a 4D image (only did so for image A previously).
    • Added utility to find blank slices and replace each with the average of the two adjacent slices.
  • VOIs
    • Fixed crash when the VOI statistics dialog is closed.
    • Fixed VOI center of mass calculation in the VOI properties dialog.
    • Much of the VOI interaction code has been refactored to more easily handle contours which span multiple slices.
    • VOI -> Mask operations now produce a new image of the type of mask generated, not the type of the original image (same for Paint -> Short mask).
  • Image views & visualization
    • Fixed some problems with the Tri-planar view's crosshairs when using the scroll wheel to move through the image.
  • Miscellaneous
    • Image header and attributes buttons have been added to the image toolbar.
    • The File and Help menus have undergone a major reorganization.
    • Scripting menu items have been moved to a new top-level menu.
    • Fixed placement of the output window.
    • Fixed the installation of .jar/.zip plugins (the directory structure of the archives are retained).
  • BIRN
    • SRB image open/save and file transfer.
    • DICOM PACS to SRB auto-upload with tag anonymization (after execution of arbitrary pre-upload script -- i.e., Face de-identification).

2.5 (05/02/2006)

  • Fixed Minc-to-Minc file saving.
  • The Open image sequence dialog (File -> Open image sequence) has been improved. Lexigraphical sorting of files is enforced and the deletion of the previously-used directory is gracefully handled.
  • Fixed the drawing of the Triplanar view (Image -> Views -> Triplanar) crosshairs and bounding box display on some image orientations.
  • Fixed a bug in the transformation (Algorithms -> Transformation tools -> Transform) of 2D images.
  • Added more interpolation methods to the Transformation dialog.
  • The MIPAV Secure chat and file transfer utility (File -> Secure file transfer & chat) has been removed.
  • (Algorithms -> Brain tools -> Face anonymization) has been renamed to (Algorithms -> Brain tools -> Face de-identification).
  • Polyline slice VOI updates -- fixed deletion, and fixed the output of slice distances.
  • VOI properties (VOI -> Properties...) now calculates values using time-slice information for 4D images.
  • Fixed the behavior of the VOI buttons when changing VOI types.
  • Improved the output of the VOI statistics dialog.
  • Fixed selection of point VOIs when zoomed in on an image.
  • Added logic to allow 4D paint-to-mask functionality.
  • An interface for a new type of "Generic" plugin has been added, allowing users to create plugins which do not require the user to open an image before using them. See the PlugInGeneric javadoc for more information.
  • Added new Maximum likelihood iterated blind deconvolution (Microscopy -> Restoration -> Maximum likelihood iterated blind deconvolution) method which works better than the old Iterative blind deconvolution (Microscopy -> Restoration -> Iterative blind deconvolution) method.

2.4 (04/17/2006)

  • Fixed an error in the image browser (File -> Image browser) when the user treid to open a series of images into separate frames.
  • A brute-force registration option has been added to the Mosaic registration tool (Algorithms -> Registration -> Mosaic).
  • A handful of bugs in the match images tool (Utilities -> Match images) have been resolved.
  • Fixed a problem with the Surface Composite view in the texture volume renderer (Image -> Views -> Volume renderers).
  • Improved handling of NIfTI files.
  • Improved handling of Bruker image files.
  • Floating point MINC files can now be saved as DICOM files.

2.3 (03/31/2006)

  • Added a tree view of the VOI structures to the VOI properties dialog (VOI -> Properties...), allowing the user to see and select individual contours on slices.
  • Improved Mosaic registration (better blending, and now works with grayscale, color and large images) (Algorithms -> Registration -> Mosaic).
  • Changed default directory of the Browse button in the Open Image Sequence dialog (File -> Open -> Open image sequence) to remember the last used directory, or use the user's home directory.
  • Fixed Image quick list keyboard shortcuts (Ctrl + num).
  • Alt + key shortcuts cannot be used anymore. Alt may be used with Ctrl or Shift.
  • Added Multi-paint tools (See the Power paint tools button at the end of the Paint toolbar), developed by Pilou Bazin at Johns Hopkins University.
  • MIPAV once again checks that the memory allocations in the LAX/preferences file match by default.
  • Slice spacing has been added to the resolutions panel of the Image attribues dialog (Image -> Attributes -> Edit attributes).
  • Added a Gabor filter (Algorithms -> Filters (Gabor)).
  • Fixed some errors writing NIfTI files.
  • When writing .img files, a dialog now pops up to ask the user whether the file should be written as Anaylze or NIfTI.
  • The interface for File Plugins has changed. See the MIPAV API documentation for more details.
  • Fixed a problem where Algorithm Plugins were sometimes launched twice.
  • Added more unique colors to the striped LUT.
  • Fixed some problems with the handling of Minc files.
  • Fixed a bug where MIPAV would freeze when the Open graph dialog (File -> Open graph) was cancelled.
  • Tri-Planar view (Image -> Views -> Triplanar)
    • Fixed an error in Tri-Planar view region grow.
    • Fixed the scale of the crosshairs in the Tri-Planar view when the user zooms in and out.
    • Added thin-plate spline and least squares registration functionality to the Tri-Planar view.
    • Fixed generation of coordinate change events when the mouse wheel is used to change slices.
    • Fixed Tri-Planar frame linking.

2.2 (03/10/2006)

  • Some bugs in DM3 file support have been found and fixed.
  • Fixed conversion of some DICOM and MINC files to NIfTI format.
  • Fixed a bug in the volume calculation of thresholded LUTs.
  • Fixed reading of XML files saved with a color LUT.
  • Gaussian blur (Algorithms -> Filters (spatial) -> Gaussian blur) in-place processing of 3D images was fixed.
  • Added the ability to replace removed slices (Utilities -> Slice tools -> Remove slices).
  • Fixed installation of .zip and .jar plugins (Plugins -> Install plugin).
  • Added scripting to:
    • VOI -> Mask -> VOI
    • VOI -> Paint -> VOI
    • VOI -> Paint -> Short mask
    • VOI -> Save VOI -> Save all VOIs
    • VOI -> Save VOI -> Save all VOIs to...
  • Fixed scripting of:
    • VOI -> VOI -> Mask -> VOI(s) to binary mask
    • VOI -> VOI -> Mask -> VOI(s) to short mask
    • VOI -> VOI -> Mask -> VOI(s) to ubyte mask
  • Fixed a bug that prevented disabling irrelevent menu items depending on the current image type.
  • A new and experimental GPU-shader-based rendering mode has been added to the Raycast volume renderer (Image -> Views -> Volume renderers).

2.1 (03/03/2006)

  • The TriPlanar view (Image -> Views -> Triplanar) has stabilized and is now fully functional.
  • A new, interactive method for registration of images into 2D mosaics has been added (Algorithms -> Registration -> Mosaic).
  • New tabs can now be created by algorithms to display output data. The contents of these tabs can then be saved to a file. This action is also scriptable.
  • Keyboard shortcut customization and handling has been improved.
  • The menus in MIPAV have been greatly reorganized and their layout has been changed slightly.
  • The font used in menus is now customizable.
  • Reading of complex image data has been added.
  • Fixed some problems with reading of GE Signa 5X files.
  • The Open File dialog now remembers the status of the Multi-file checkbox between MIPAV sessions.
  • Minc file attributes can now be anonymized (both dicom-converted attributes and minc-specific attributes).
  • When saving a Minc file to Dicom, any dicom-converted attributes in the Minc header are retained in the new Dicom file.
  • The Dicom Save dialog now provides a button that fills in required tags with auto-generated data.
  • Support for the DM3 file format has been added.
  • Fixed a number of problems in the handling of NIfTI files.
  • Added option to show the name of VOIs name instead of their label.
  • The user's VOI XOR preference is now correctly retained.
  • A greatly improved Face Anonymization (Algorithms -> Brain tools -> Anonymize face) algorithm has replaced the old method.
  • A label in the LUT window (LUT -> Histogram - LUT...) now shows the thresholded voxel volume.
  • Scripting fixes:
    • Algorithms -> Brain tools -> Extract brain surface (BET)
    • Algorithms -> Brain tools -> Extract brain surface (BSE)
    • Algorithms -> Filters (spatial) -> Gaussian blur
    • Algorithms -> Filters (spatial) -> Gradient magnitude
    • VOI -> Statistics generator...
  • Volume renderer (Image -> Views -> Volume renderers)
    • Button to enable all clipping planes.
    • The clipping planes can now be used to remove data from the original image volume.
    • 3D stereo view of the volume is now available.
    • Improved ray-cast renderer performance by 20-30 percent.

2.0 (02/01/2006)

  • MIPAV is now packaged with Java 1.5 (also known as JRE 5.0), Java3d 1.4beta3, and JMF 2.1.1e. Solaris remains packaged with Java 1.4.2 and an older version of Java3D. In the future Solaris releases of MIPAV may not install a JVM. The Macintosh release of MIPAV remains the same, working with Mac OS X 10.3 or higher (JVM 1.4 or 1.5).
  • The user's choice of toolbars is now remembered automatically when selections are made in the Toolbar menu.
  • A -m option has been added to open multi-file images from the command line.
  • Fixed a problem with the Shortcut editor (Help -> Shortcut options).
  • Skeletonize requires 2.5D processing of 3D images.
  • Bug in Transform algorithm's (Algorithms -> Transform) matrix inversion has been fixed.
  • Watershed algorithm (Algorithms -> Watershed) energy file reuse fixed.
  • Fixed scripting of face anonymizer.
  • The Image Math dialog (Algorithms -> Image math) now can calculate the absolute value of an image or the average value of all of a volume's slices.
  • Improved DICOM file reader and header parser.
  • Fixed a bug in the writing of DICOM files from MIPAV.
  • NIfTI file handling changed and improved significantly. Please email us with any problems you encounter.
  • Handling of MINC files has also been improved.
  • The user can now change the resampling method when opening the Volume Renderer view (Image -> Views -> Volume renderers).
  • VOI changes:
    • Added the ability to delete the active point from VOI contours by pressing SHIFT + DEL.
    • VOI line info can be printed out through CTRL + left click.
    • Moving VOIs around updates the user interface with the active point's current location.
  • The Tri-Planar view (Image -> Views -> Triplanar) continues to improve and is nearing completion:
    • All VOIs and painting should now work in this view.
    • Added option to use old view (which is remembered whenever the Tri-Planar view is opened).
    • Methods ending in _XY, _ZY, and _XZ have been changed to _AXIAL, _SAGITTAL, and _CORONAL (constants with those names changed too).
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