MIPAV change list 1.xx

• The functionality provided by the Dual Tri-Planar view has been collapsed into the Tri-Planar view (Image -> Views -> Triplanar). When a second image is loaded, the Tri-Planar image display changes to show both images, shown as it was in the Dual Tri-Planar view. Region growing and bounding cube operations are still being refactored and do not function correctly in this release. Position information is now shown in a separate window accessible from the menu item (Options -> Show volume coordinates and talariach controls) in the Tri-Planar frame.
• Added the ability to read and save surfaces in a new XML format.
• Scripting support has been added the the Fill Objects algorithm (Algorithms -> Morphological -> Fill holes)
• Scripting and user-defined ranges are now supported by the Replace Value utility (Utilities -> Replace pixel/voxel value).
• Nearest neighbor output interpolation has been added to the various OAR registration methods.
• Image subsampling (Utilities -> Subsample) now supports transforming VOIs within the image.
• Show costs (Algorithms -> Registration -> Display pixel similarity cost functions) now supports 2D images.
• Fixed the VOI perimeter statistic in the VOI property dialog.
• A new image padding utility has been added (Utilities -> Pad with slices)
• A bug in adjusting the paint opacity has been fixed.
• Fixed an issue with 0 to 1 LUT adjustment for image B.
• Point VOIs can now be shown as one of four different images: normal, normal with the center pixel removed, an X, and an X with the center pixel removed. Which one is used can be changed through the MIPAV Options dialog (Help -> Program options).
• Selected VOI points can now be adjusted through use of the arrow keys.
• 2.5D processing is now supported in the Skeletonize algorithm (Algorithms -> Morphological -> Skeletonize).
• Handling of multi-file images when loading a second image into a frame is now consistent with the process for reading in the first image.
• A number of bugs in the Light Box view (Image -> Views -> Light box) have been addressed.
• Miscellaneous bug fixes and improvements have been made in the following areas:
  • Algorithms -> Segmentation -> Graph based
  • Algorithms -> Threshold
  • Algorithms -> Transform
  • Algorithms -> Transform to power of 2
  • Utilities -> Add image margins
  • Utilities -> Insert slice
  • Utilities -> Match images
  • Utilities -> Noise

• Fixed a problem when running the software when the MIPAV configuration directory does not already exist ($HOME/mipav), which would prevent MIPAV from running unless the directory was manually created. If not found, it is now created automatically.
• The TriPlanar view (Image -> Views -> Triplanar) has been greatly improved and most functions should now function correctly. Coordinate display, mouse wheel navigation, painting, and VOI operations for all image orientations now work.
• When the TriPlanar view is open, clicking with the middle/scroll button in the original image will center the TriPlanar view at the clicked point.
• If MIPAV is run without a GUI (i.e., with the -hide option), encountering an error will cause the software to exit with an abnormal value (1).
• Snap-to-pixel behavior while painting has been finished and is no longer an option that can enabled or disabled.
• Both active and non-active scripts generated by MIPAV can now be used interchangeably.
• The Crop utility (Utilities -> Crop) now always creates a new image.
• Opening the Volume Renderer (Image -> Views -> Volume Renderers) by clicking the padding button when no padding is necessary no longer causes an exception.
• Miscellaneous bug fixes and improvements have been made in the following areas:
  • Algorithms -> Fuzzy C-means -> Multispectral
  • Algorithms -> Histogram equalization -> Neighborhood adaptive
  • Algorithms -> Histogram equalization -> Regional adaptive
  • Algorithms -> Image calculator
  • Algorithms -> Extract brain -> Extract brain surface (BSE)
  • Algorithms -> Morphological -> Particle analysis
  • Algorithms -> Registration -> Constrained optimized automatic registration
  • Algorithms -> Registration -> Optimized automatic registration
  • Algorithms -> Registration -> Optimized automatic registration 2.5D
  • Algorithms -> Registration -> Optimized automatic registration 3.5D
  • Algorithms -> Registration -> Landmark -> Least squares
  • Algorithms -> Transform
  • File -> DICOM browser
  • Writing of some TIFF image files.

• Multifile and single file images are now opened from the same menu item (File -> Open new image(A)) and how an image is opened is controlled by a checkbox in the File Selection dialog.
• Fixed a number of issues when using MIPAV to receive DICOM images over a network (File -> DICOM receiver on/off).
• The drawing and display of images has been greatly improved. It is now faster, with reduced flicker when moving VOIs and the mouse cursor. The interpolated mode of displaying images has also been updated, allowing for either image A or image B or both to be interpolated independently and making it so that paint on an interpolated image does not appear interpolated (blurry). Work on updating the TriPlanar view (Image -> Views -> Triplanar) to make use of these improvements is continuing and should be available in the next version of MIPAV. Users who need to paint or perform other operations in the TriPlanar view besides simply viewing images should not upgrade at this time.
• An option in the MIPAV Options dialog (Help -> Program options) now allows for the user to choose whether the paint cursor should exhibit snap-to-pixel behavior.
• Added Haralick texture feature measurements algorithm (Algorithms -> Filters (spatial) -> Haralick texture).
• Added a utility which will replace all occurrences of one value in an image with another value (Utilities -> Replace value).
• A number of algorithms have been fixed:
  • Algorithms -> Edge detection -> Zero X laplacian
  • Algorithms -> FFT
  • Algorithms -> Filters (frequency)
  • Algorithms -> Filters (spatial) -> Mode
  • Algorithms -> Filters (spatial) -> Nonmaximum suppression
  • Algorithms -> Filters (spatial) -> Unsharp mask
  • Algorithms -> Fuzzy C-means -> Multispectral
  • Algorithms -> Shading correction -> Inhomogeneity N3 correction
• Running scripts on multiple images from the command line has been fixed.
• Work is continuing on updating and improving Volume Renderer (Image -> Views -> Volume renderers).
• The Volume Renderer now has been tested with the latest versions of Java 1.4 and 5.0 (1.5) on Mac OS X 10.4.

• The Load Image dialog (File -> Load -> Image(B) from frame) now has the "Match orientations of two images." and "Use image origin information to align images." default to being selected.
• The Save As dialog (File -> Save image as) now defaults to the image's filename.
• Fixed the handling of the image resolution when saving an XML file from a DICOM image.
• Two 2D images can now be matched (Utilities -> Match images).
• Multi-file images can now be opened from either the Open Image dialog (File -> Open new image(A)) or the Open Multi-file dialog (File -> Open multi-file(A)) through the use of a checkbox.
• Reduced the amount of flicker of progress bars and defaulted them to appearing in the center of the screen.
• Added snap-to-pixel logic for the paint brush cursor.
• The Paint Grow dialog has been improved, among the changes are better support for region grows in color images and from the Dual-Triplanar view (Image -> Views -> Triplanar - dual)

• Many of MIPAV's keyboard shortcuts can now be used when an image frame is selected, not just when the main UI window is selected.
• A Graph-based segmentation algorithm (Algorithms -> Segmentation -> Graph based) has been added.
• The Extract slices (Utilities -> Extract slices / volumes) utility now provides more information to the Output window when run.
• A new set of "power" paint tools have been added to the paint toolbar.
• When the order of slices is randomized (Utilities -> Randomize slice order), the slice mapping is now printed to the data tab of the Output window.
• The paint grow dialog now allows the user to enter in arbitrary upper and lower threshold deltas.

• Choosing an image out of a multi-file image set through the File -> Open new image(A) menu item now only opens that image, not any of the others in the series. To open the full multi-file image set, use the File -> Open multi-file(A) menu item. Multi-file image sets show up in the recently used images list of the File menu with (M) appended to their file name.
• The DICOM reader has been fixed so that images with singular transformation matrices can still be read.
• The Rotation utility now correctly sets the new image's orientation.

• Plugins packaged in jar or zip files can now be installed through MIPAV (Plugins -> Install plugin). The class files in these archives are unpackaged into the MIPAV plugin directory in the user's home directory.
• Fixed an error when the user canceled the dialog which allows for the loading of a second image from a file.
• Clicking the New Mask toolbar button with a color image now creates a mask image that is also a color image-type.
• Fixed the display of the count in the logarithmic mode of the Histogram (LUT -> Histogram - LUT).
• Changing the window and level functions by clicking and dragging in the image window now works for color images.
• The user can now open an image's header information (Image -> Attributes -> View header) by pressing CTRL-H while the image's window is selected.
• The user can now open an image's image information editing dialog (Image -> Attributes -> Edit attributes) by pressing CTRL-E while the image's window is selected.
• A problem in the DICOM receiver (File -> DICOM database access) has been resolved and debugging output has been updated to only appear when the "Comms" debugging option is turned on.
• Added support for the reading of the DICOM YBR_FULL_422 JPEG compressed images.
• Reading and writing of DICOM RGB images has been improved.
• Improved the saving of DICOM files, most notably by saving in lexigraphically correct order of image file names (e.g., foo0001.dcm, foo0002.dcm, ..., foo0010.dcm, ...).
• Saving/opening of linked images has been fixed.
• Fixed the reading of MINC label files.
• Fixed an issue reading some LSM image files.
• The MRC image handler now writes image header information correctly when only a subsection of the slices are saved.

• The Mask utility (Utilities -> Mask) now works with color images.
• Fixed the copying of image headers after slices are removed (Utilities -> Remove slices).
• Fixed an issue in the numbering of anonymized images (File -> Anonymize DICOM directory).
• Fixed a minor issue in the ordering of VOIs in the VOI Extraction algorithm (VOI -> Mask -> VOI).

• The reading and writing of a number of different image types has been greatly sped up. The speed of some algorithms which do many image buffer imports and exports has also been improved.
• Improved the adding of linked images in MIPAV XML image files.
• A new system for specifying the amount of debugging output to display has been added to the options dialog (Help -> Program Options). Current options include minor, algorithm, file and communication messages.
• We are continuing to refactor and improve the volume renderer (Image -> Views -> Volume renderers) and its opacity controls.

• Fixed bug in handling of some LSM files.
• Fixed a bug in the reading of some TIFF files.
• Fixed a problem where MINC images were being written out upside down.
• Improved the memory management of VOIs.
• Resolved problem with the alpha blending of fused images within the volume renderer.

• The appearance of a number of windows on Mac OS X has been fixed, including the Tri-Planar view and the Volume Renderer.
• Image frames, the Output window, and the Animation window now have new icons which differentiate them from the main user interface window in the taskbar.
• Image Math (Algorithms -> Image math) now handles complex images.
• The Image Calculator (Algorithms -> Image calculator) no longer destroys phase information when clipping complex image values.
• Flipping (Utilities -> Flip) now works with complex images.
• Handling of LSM files has improved slightly.
• Fixed bugs when opening or closing masks generated from the Paint Toolbar.
• The flexibility of the Image Sequence Loader (File -> Open image sequence) continues to improve.
• Fixed a bug in the zero-padding of filenames in the DICOM receiver (File -> DICOM database access).
• Fixed an error in the labeling of VOI contours created by the Rubberband Livewire method.
• Fixed the loading of the linked image when an image is opened using the Recently Used Image list.

• MIPAV has a new splash screen.
• The UI no longer is displayed when the -hide option is used from the command line.
• Improved memory management in the Image Sequence Loader (File -> Open image sequence).
• Added an option to load any grayscale image scaled to the range 0-255 from the Image Sequence Loader (File -> Open image sequence).
• The LightBox, Tri-Planar, and Volume Renderer views now each have special icons which are displayed in the corners of their windows and on the taskbar.

• Holding down the 'Q' key now enters Quick LUT mode.
• Images can now be subsampled as they are being loaded from the Image Sequence Loader (File -> Open image sequence).
• Window and Level adjustment sliders have been added to the Image Sequence Loader.
• Added the option to add blank padding slices to an image volume to have the dimensions be powers of two when loading it into the Volume Renderer (Image -> Views -> Volume renderers).
• Added a surface area calculation to surfaces within the Volume Renderer.
• When switching between surfaces in the Surface tab in the Volume Renderer, the opacity and shininess sliders now update correctly.
• The behavior of the Particle Analysis algorithm (Algorithms -> Morphological -> Particle analysis) has been fixed.
• The menu items for RGB -> Gray, RGB -> Grays, RGB -> HSB, and Grays -> RGB in the Utilities menu work correctly once more.
• Fixed an error where the image produced from an AND mask operation did not have the original image's attributes.
• Enhanced the LSM file reader to handle Ziess format 3.5.
• Fixed a bug related to an assumed directory structure in the XCOSM algorithm (Algorithms -> Microscopy -> Restoration -> XCOSM_EM).
• Improved the BET Brain Extractor (Algorithms -> Extract brain -> Extract brain surface (BET)) segmentation slightly.
• Constructors for FileIO and ViewJFrameImage which take ViewUserInterface objects have been deprecated. All other constructors which take ViewUserInterface will be deprecated over the course of the next month or so. Eventually, these constructors will be removed completely. ViewUserInterface has been changed to be a singleton class, meaning that there is only one occurance of it anywhere within MIPAV. The practical upshot of this is that plugin writers will have to adjust to use the new constructors as they are added, and use the function ViewUserInterface.getReference() if they need to use the user interface for something.

• Ctrl-C/X/V now copy/cut/paste selected VOI contours within an image.
• The DICOM/image overlays have been improved, allowing for prefix strings to be added to tags displayed in the image.
• Running the Median filter (Algorithms -> Filters (spatial) -> Median) on VOI regions has been sped up significantly.
• Fixed resetting of the LUT when painting into a image, when the paint intensity is between the image's min and max values.
• The dialog used to open multi-channel Image Sequences (File -> Open image sequence) (formerly the TIFF Image Sequence dialog) now handles all image types and has had a number of other improvments.
• An option has been added to the FRET efficiency algorithm (Algorithms -> Microscopy -> FRET efficiency) to show the efficiency image.

• A method for opening multi-channel TIFF image sequence has been added (File -> Open TIFF sequence).
• Added an algorithm to attenuate an image along the boundaries of VOIs placed within it (Algorithms -> Filters (spatial) -> Boundary attenuation).
• Whether the DICOM and/or image overlays should be shown is now saved in the MIPAV preferences file and remembered at each startup (Image -> Show image/DICOM overlay).
• Buttons to open and save a user-defined LUT have been added to the main MIPAV toolbar.
• The Transformation dialog (Algorithms -> Transform) now allows for the matrix which will be used to be automatically inverted before the transformation is applied.
• Some of the menu items have been altered slightly, so that their names make some more sense and the capitalization scheme is followed consistently.
• Resolved some issues reading in LSM files.
• Improved memory usage of Coherence Enhancing Diffusion (Algorithms -> Coherence-enhancing diffusion).
• Fixed auto-rotation image capture of the Raycast Renderer (Image -> Views -> Volume renderers).
• Fixed sizing of the Tri-Images in the Volume Renderer (Image -> Views -> Volume renderers) when the window is maximized.

• The MIPAV API documentation has been updated and is available online.
• The DICOM Receiver now pads the instance number of received images.
• A new Paint toolbar button has been added to allow for the paint on the current slice to be erased. Another button erases all of the paint in the image volume.
• The undo button on the Paint toolbar now reverses one level of any paint change (including region growing).
• The FFT (Algorithms -> FFT), Autocovariance (Algorithms -> Autocovariance coefficients) and Autocorrelation (Algorithms -> Autocorrelation coefficients) algorithms no longer crash when run.
• Fixed a bug in the viewport clipping plane, in the Volume Renderer (Image -> Views -> VolumeRenderers).
• Histogram Summary (Utilities -> Histogram summary) can now be run on the entire image or just VOIs.
• Improved handling of nested objects and holes in VOI to mask conversion.
• Dragging of non-contour VOIs has been fixed.
• The MIPAV splash screen now displays the version of MIPAV in the title bar.
• In the SUV PET Plugin, more parameters are available for user review and modification.

• The Image browser now properly cleans up the preview images it uses and removes them from the image registry.
• An option has been added to the 3D OAR Registration (Algorithms -> Registration -> Optimized automatic registration) method to perform a Least Squares registration (Algorithms -> Registration -> Landmark - Least Squares) and then a OAR registration on the resulting volume.
• When running a script in MIPAV from the command line, relative paths to images specified with -i will be searched for in the current working directory of the user's terminal when he or she runs MIPAV. This directory will be set to be the new default directory for MIPAV to look for images in, the default directory will also be changed to the path to an image the user specifies with -i if the path is absolute.
• When the -hide option is specified, the text which would appear in a dialog if MIPAV was running normally is now printed to the terminal's standard error.

• A crop function has been added to the VOI pop-up which appears when a VOI is right clicked.
• When raycast rendering in the MIP and DDR modes in the Volume Renderer, fixed an issue which caused the LUT to not update when changed.
• Simplified method calls needed to change the image displayed by the TriImage and DualTriImage views. Only calls to the methods setImageA() and setImageB() should necessary.
• An error in the Inhomogeneity N3 Correction (Algorithms -> Shading correction -> Inhomogeneity N3 correction) algorithm has been corrected.
• DCCIE convertsion (File -> DCCIE Image Conversion) now copies TIFF files from the old directory to the new directory automatically.
• The DICOM parser now properly handles tag 0018,1164 Imager Pixel Spacing.
• Fixed exception which happened when transforming (Algorithms -> Transform) an image and its VOIs.
• Mask images are now created with the correct file information from the original image.
• Dialogs with Gaussian fields, now accept values in the range (0.0 - 10.0) instead of (0.5 - 5.0).
• When dialog parameter saving is enabled in the Program Options (Help -> Program Options), dialogs which normalize the Z scale of gaussians no longer save the normalized value.
• The Nonmaximum Supression algorithm (Algorithms -> Filters (spatial) -> Nonmaximum suppression) now saves its parameters when the feature is enabled in Program Options.

• Scrolling the mousewheel in the Tri-Planar view now changes the displayed slice.
• The user can now change the image slice displayed from within the Surface Plotter view.
• Right clicking on the zoom buttons on the toolbar allows the user to change between exponential (1x, 2x, 4x, 8x, ...) and linear zoom (1x, 2x, 3x, 4x, ...) increments.
• Fixed a bug which caused the Tri-Planar view to initially display a different slice of an image than shown in the position labels.

• The plane displayed by the arbitrary clipping pane in the Volume Renderer (Image -> Views -> Volume Renderers) can now be extracted to a new image.
• Fixed a bug where image origin information was not being copied when a mask was extracted from a VOI (VOI -> VOI->Mask).
• Fixed bug which prevented opening of DICOM files once a DICOM image was cloned.
• Added paint propagation buttons to the paint toolbar (Toolbars -> Paint toolbar).
• Added a new color LUT optimized for display of bones in the Volume Renderer.

• A memory usage monitor and garbage collection button have been added to the main MIPAV window.
• The Zoom controls now only perform one magnification / de-magnification when the user clicks in the image. Holding down Shift allows for multiple Zoom actions. Right clicking in the image does the opposite of the selected Zoom action. (i.e., If Un-Zoom mode has been selected, right clicking would cause the image to zoom in, while a left click would un-zoom the image.)
• Fixed issue reading in some TIFF files.
• Added support for an additional method of identifying data type for BRUKER files (e.g., ip_short).
• The algorithm history log now includes a timestamp.
• Cropping (Utilities -> Crop) can now be performed by using a VOI or entering parameters into a dialog.

• Fixed handling of saving unsigned short DICOM files to Analyze format. These files are now saved as signed short Analyze files since unsigned short DICOM images typically range between 0 and ~1000. MIPAV will now also read in the non-standard-compliant unsigned short Analyze images which some previous versions of MIPAV would save.
• More improvements have been made to the DICOM browser (File -> DICOM browser).
• If an image's units or Z dimension resolutions differ by more than a factor of 20, a warning dialog is brought up.
• Fixed loading of multi-image sets when the numbers in the file names are not padded with zeros.
• Added scripting support to Least Squares Registration (Algorithms -> Registration -> Landmark - Least Squares).
• Added scripting support to Thin Plate Spline Registration (Algorithms -> Registration -> Landmark - TPSpline).

• The DICOM browser's (File -> DICOM browser) table display of DICOM tags has been improved. It can now be configured to show custom tags, the columns can be rearranged by the user and the tag columns are sortable.
• Replace Slice (Utilities -> Replace slice) allows the user to replace a slice with another open image.
• Saving of point VOIs fixed.
• Histogram calculation for images with a large range of values has been sped up.
• Talairach VOI extraction bug fixed.
• Button added to toolbar for inverted masking of the currently selected VOI contours.
• BET (Algorithms -> Extract brain -> Extract Brain Surface (BET)) initial sphere size tweaked slightly.
• Utilities -> Invert now displays a dialog which gives the user the option of placing the inverted image in a new frame or the source image frame.

• New PDFs of recent MIPAV course presentations have been placed in the documentation section of our website.
• Mac users no longer need to install Java WebServices.
• The Image Calculator (Algorithms -> Image Calculator) now works with complex images.
• The default directory for saving files is now the directory of the currently open image.
• Fixed user defined lut and transfer function save/load.
• Scripting support added for extract slices volume.
• Added ability to put a prefix on images saved within a script.
• The splash screen no longer shows up when MIPAV is run with the -hide option.
• Fixed bug closing image frames in a script.
• Fixes made in AFNI file support.
• VOI -> Paint Mask now only operates on selected voi contours.
• Polyline VOIs can now be closed into polygons.
• Arbitrary clipping plane behavior in the Volume Renderer has been fixed.
• Texture aligned rendering mode available again in 3D texture rendering.
• Fixed talairach position information display in tri-planar view.

• The Algorithms -> Extract brain -> Extract Brain Surface (BET) and Algorithms -> Extract brain -> Extract Brain Surface (BSE) algorithms can now optionally extract the brain as paint instead of masking off the brain from the original image.
• On Windows systems, the MIPAV installer now places msvcp71.dll and msvcr71.dll, which are required by the ITK libraries, into %SystemRoot%\System32 if they are not already located there.
• More improvements to Dicom file handling.
• VOI -> Paint -> Mask now works for 2D and 3D images.
• The VOI statistics file is now saved in the current image's directory.
• VOI Statistics (VOI -> Statistics Generator...) and Properties (VOI -> Properties...) now handle XOR VOIs correctly.
• A number of fixes to the Histogram (LUT -> Histogram - LUT) dialog when imageB is loaded.
• The masking intensity button on the paint toolbar has been replaced by a spinner.
• Opening an image from the recently opened image list now sets the current default directory to that image's directory.
• More improvements to Talairach support.

• Fixed handling of encapsulated JPEG Dicom files.
• "QuickMask" Utilities -> Mask shortcut button added, which runs the mask algorithm with the default parameters.
• Holding down Crtl while in paint mode erases paint.
• Added Mask -> Paint conversion menu item.
• LUTs are now 1-based by default.
• An image of the LUT with transfer function points indicated on it can be saved to disk (LUT -> Histogram - LUT).
• Points on the transfer function can now be redistributed at even intervals.
• Fixed reading of VOI files for which the user does not have write permission.
• The VOI statistic dialog (VOI -> Statistics Generator...) is now scriptable.
• VOI statistic information can now be saved to a location the user specifies as a text file.
• Fixed error when opening the lightbox view (Image -> Views -> Light Box).
• More talairach fixes have been made.
• Algorithms -> Extract Surface -> Cube has been renamed to Algorithms -> Extract Surface (marching cubes).
• The extract surface dialog now allows the user to select the format that the surface mesh is saved as (either text (.txt), surface (.sur), or VRML (.wrml)).
• In the extract surface dialog, the surface file directory is now shown in the tooltip of the surface file name.
• Improvements have been made to the surface boundary view in the volume renderer's plane renderer.
• Added $home/mipav/plugins and $home/mipav/plugins/plugins.jar back into MIPAV's classpath.
• Fixed error when starting mipav when $home/mipav/mipav.preferences doesn't exist.

• Talairach support improvements:
  • MIPAV's XML image header now includes a section containing Talairach information.
  • Talairach tab added to the image attributes dialog (Image -> Attributes -> Edit attributes).
  • Tri-planar view (Image -> Views -> Triplanar) now loads the image into Talairach space when the information is present in the image's XML header.
  • Talairach information can be read from Medic's file format into the Talairach section of MIPAV's XML header.
  • The transformation dialog (Algorithms -> Transform) can now transform an image with Talairach information into Talairach space.
• The layout of the Image Browser (File -> Image browser) has been improved.
• The Image Browser now shows .tiff files.
• When saving (File -> Save image) an image to a file name which already exists, the user is now prompted before the file is overwritten.
• The Zoom In and Zoom Out toolbar buttons now stay activated after the user's first click in the image (holding down Shift is no longer necessary).
• The sharpness of the paint border has been improved when an image is being shown in interpolated mode.
• The user can now switch to a 1-based LUT (LUT -> Histogram - LUT).
• Fixed a number of NullPointerExceptions in the image and tri-planar image frames.
• Preliminary support for invocation of ITK methods from within MIPAV. See Algorithms -> Insight Toolkit -> Gaussian blur for an example. ITK dll files are included with the Windows release of MIPAV. Users on other platforms must compile the ITK libraries and Java bindings and place them in /path/to/mipav/InsightToolkit/bin/.

• A new option has been added to the command line. -o (or -O) allows the user to specify the name of an output file for the scripting command SaveImageAs. Usage example:

     save.sct:
     SaveImageAs $active .xml
     Exit

     C:\>"C:\Program Files\mipav\mipav.exe" -i c:\images\oldimg.xml -s c:\images\save.sct -o newimg -hide
     This would read in oldimg.xml and save it as newimg.xml.

• The CT Presets dialog has been altered to allow the user to specify a custom set of thresholds for CT images.
• A number of useful image masking tools have been added to the paint toolbar.
• The behavior of the Zoom In and Zoom Out toolbar buttons has been changed. The user must now click within the image, causing it to change the image's magnification while centering the image on the clicked point. Holding the Shift key while clicking allows the user to Zoom In or Out multiple times.
• The user can now center the image window on a specific point by holding down Control when clicking within the image.
• Holding down the shift button while in paint mode allows the user to move the mouse to paint without holding down the left mouse button.
• The Program Options dialog (Help -> Program Options) has been reorganized and the color of the VOI rubberband can now be altered.
• Histogram Summary (Utilities -> Histogram summary) now allows the user to specify a number of bins.
• Clean-up done when closing MIPAV has been improved.
• MIPAV no longer save or read unsigned short analyze image headers (which are not allowed by analyze specification).
• The paint toolbar now defaults to having the thickest paint brush size selected.
• Fixed bug in the painting of the paint eraser border.
• Fixed problem moving a point of a line VOI.
• Batch conversion of uncompressed AVI files to compressed AVI files has been added to DCCIE Image Conversion (File -> DCCIE Image Conversion).
• Attempting to read in a DICOM image which does no longer creates a zero-byte file.
• The Volume Render (Image -> Views -> Volume Renderers) continues to be improved.

• Included Linux JRE is now version 1.4.2.07, the JAXP included is from JWSDP 1.5, and Java 3D has been upgraded from Blackdown's 1.3.1 beta, to their final version 1.3.1
• VOIs and VOI calculations (VOI -> Properties)
  • Changes to the statisticial reporting of perimeter of VOIs and errors in the second order attributes of contour VOIs were fixed
  • Center of Mass calculations are now based on area
  • Major-axis and minor-axis calculations have been included for elliptical VOIs on 2D images
  • Save-All VOIs should now correctly write the list out
• Fibroid plugin
  • Displays both moments and perimeter fitting for 2D images, however, 3D images will only display moments fitting
  • Now returns information on all the axes for 2D and 3D ellipsoid diameters
• Plane-rendering (Image -> Views -> Volume Renderers)
  • When the user adds or removes surfaces to the 3D texture volume view, the three plane renders show the boundary of the surface with specified color accordingly
  • Mouse behaviors changed:
    • Shift + left mouse press --- Translate
    • Left mouse press only --- Viewing coordinate changes
    • Middle mouse press --- Zoom
• DICOM images with floating-point slope and intercept now correctly load the image-data
• Overlaying a grid onto an image with selectable color and independent x and y resolution based width and height
• Cardiology VOI improvements
• DICOM Browser has a new option to allow user to ignore series number in order to load all DICOM slices of the same study ID into an image. (primarily for cardiology people)
• NEI Segmentation Plugin update
• MRI Shading correction (Algorithms -> Shading Correction -> MRI combined info) has been added
• Automatically generated Filename lists no longer include directories
• We now can display histograms of Images using Color, unsigned-short data
• Units have been added to the output; "degrees" now follows the principle axis calculation output.

• Morphological filtering (Algorithms => Morphological -> Morphological Filter)
• Homomorphic filtering (Algorithms -> Filters (Hormomorphic)) on monochrome images
• Nearest-neighbor interpolation is now available in the Interpolation routines in the Transform dialog (Algorithms -> Transform) for single-slice (2.5D) images
• The image calculator (Algorithms -> Image Calculator) now supports finding minimums; the functions' order has been made alphabetical
• EM colocalization (Algorithms -> Microscopy > Colocalization -> Expectation Maximization) now produces a segmented image with zero values for those pixels excluded because they do not meet threshold conditions and a different nonzero gray value for each Gaussian class
• The QUADPACK DQAGE globally adaptive integrator routine for integrals without singularities or infinite bounds has been implemented. The most useful 4 of the 9 routines have now been implemented
• Improvements to Inverse Laplace Weeks now prevents error from going to infinity.
• The RFA Volume calculation tool can now calculate the exact burning volumes for the removal of selected burn-points
• Changes to Entropy minimization(Algorithms -> Entropy Minimization)
  • Speed improvement, but no longer writes as much debugging information
  • The mean intensity is now preserved in the transformation process
  • dialog now allows the user to specify a threshold for excluding peripheral background pixels from the transformation process
  • The dialog now has a default enabled user checkbox for image subsampling in histogram formation to speed up program execution
  • Choice of either: multiplicative and additive quadratic noise, multiplicative quadratic noise only or cubic multiplicative noise
• Fixed:MINC writer now correctly saves 3D DICOM files
• The Dual Triplanar view has been updated to display patient position information, if available, and integrate point translation changes from the regular Triplanar view
• Preferences now does not re-read the mipav properties file every time a data accessor function is called (fixing a problem with too many open file handles on the linux platform)
• Surfaces are no longer pickable by default when loaded into the volume renderer.

• Automatic Mid-sagittal alignment algorithm (Algorithms -> Midsagittal Line Alignment)
• Option to save a MIPAV-format XML header file of image information when saving Analyze-formatted image files
• Update to the interfile format to open additional files
• FSL NIFTI file format support has been included to NIFTI support
• Volume rendering upgrades
• Calculation of volume around burn-points for RFA now provide output in voxels surrounding the burn-point
• VOI cardialogy tool added (in unfinished form) to assist segmentation and quantification of heart images (VOI -> Cardiology VOI)
• Added VOI behaviors for selection, copying and grouping
• Change to the about.txt file to include two previously unrecognized developers
• Faster DICOM file reading
• Fixed: Paint border correctly displays around images of unknown orientation in the triplanar view
• Fixed: Image Transformation (Algorithm -> Transform) again supports single-slice (2.5D) images
• Rotate scripts fixed
• Fixed: Matrix decomposition should now print the translations correctly

• Triplanar View:
  • Pixel indexing no longer starts with zero (0) but starts with one (1)
  • labels no longer get positioned off the image and disappear under the frame
  • Axis orientation labels now provide Anterior/Posterior, Inferior/Superior and Left/Right information for the three-plane orientation when the orientation information is known; otherwise, the old X, Y and Z axis labels are used;
  • For DICOM images, position information is now displayed correctly
  • Region grow is now fixed
• Paint changes:
  • The key [B] now toggles a paint border
  • The keys [1] through [4] allow the user to temporarily change the paintbrush to the size indicated by the keypress. [1] is smallest and [4] is the largest brush; the paint tool will use the brush for as long as the key is pressed and will revert to the menu-selected brush;
  • Opacity dialog is no longer modal and will update the slider as a change is made
  • Paint -> Short Mask (VOI -> Paint->Short Mask) now builds a short mask
• VOI changes:
  • [CTRL]-[SHIFT] selects multiple contours & multiple VOIs
  • [CTRL] alone selects contours
  • Group (VOI -> Group VOIs) selects only the selected contours to form a new VOI
  • Select All VOIs (edit -> Select All VOIs) select all VOIs in the image
• RF probe can move (translate) along the directional axis as well as rotate about the entry burn-point to allow the user to reposition the probe from within the entry, rather than making multiple entry points
• MIPAV now searches for its preferences and plugins from within a subdirectory of the installing user's home directory called mipav. Users who upgrade from a previous version of MIPAV should see no other difference except for the new mipav directory. The old preferences will be copied into the new directory.
• The setting for InstallAnywhere to create a 64-bit Itanium Windows installer has been set

• VOI changes:
  • Mask generation:
    • Mask images with holes can be converted into VOIs with holes
    • VOIs also may generates mask images with holes; masks can generate either VOIs with holes or VOIs without holes;
    • default is to ignore holes
  • Border is painted around a painted VOI to indicate edge of VOI
• Paint changes:
  • Paint tool uses a sized cursor to indicate location of paint area
  • toolbrush sizes have changed -- the largest brush is now larger. The sizes are now (square): 1, 4, 8 and 16 pixels square
• Volume Renderer changes:
  • Sculpting of the 3D images is now possible for RayCasting and ShearWarp visualisations
  • Geodesics (lines on the surface) may now be drawn onto a surface
  • we can now find length information on a surface
• Match Images uses less memory
• Talairach help is now available within contextual help in MIPAV; the HOWTO also includes information on Talairach
• Scripts can now call plugins
• DICOM can now read Dynamic PET DICOM-formatted images
• Interpolation option within the Histogram option has been sped up 4 - 5 times to operate on an image at speeds which are almost un-noticable.

• Plugins classpath changes:
  • MIPAV has changed where it loads plugins: plugins are now loaded from the mipav_plugins directory under the user's home;
  • plugins.jar in the same place (mipav_plugins) is added to the search path, however MIPAV does not currently load jar files as plugins
• Opacity changes to the LUTs
• Volume Renderer includes extra modes
• QTjava.zip (QuickTime library) is not needed by MIPAV and has been removed from the distribution

• Plug-ins change now correctly sets the classpath and properly places the plugins within the directory plugins within the MIPAV installation

• MIPAV no longer queries Macintosh users to accept any memory changes on each startup.
• Plugins have changed to allow plugin programmers to install plugin class files from a plugins directory within the user's home direcory.
• 2D and 3D Fill Holes has been added to the morphology toolset
• A number of 3D user-interaction changes; expect more in future releases
• Triplanar view orientation bugfix; some enhancements too

• Non-linear b-spline registration:
  • two pass
  • Operates on 2D, 3D and 2.5D (slice-by-slice)
  • Added cost functions:
    • correlation ratio
    • Normalisaion MI
  • Color support
• Changing the location of a point on a VOI now makes the mouse cursor and the point dissapear to make it easier to see the VOI
• Scroll button on the mouse now scrolls through the image slices of a 3D image
• The scripting box now displays the full path to the image and VOI files in a tooltip because sometimes the list is not large enough
• Scripts can now save data from the Global Data and the Data output panes
• BSE documentation updated
• VOI copy operations from different source and destination images now retain the original VOI name
• TIFF loader now understands LZW Compressed formats
• RFA Probe displays text tags when the probe has passed through hard tissue
• DICOM to XML image format dialog now allows the tags to be sorted based on tage name
• Version number in about file is incorrect

• Surface rendering of the RFA probe is smoother
• Script logging has been improved
• Updated scripting documentation
• G.E. to DICOM converter
• On-image text annotation added; allows user to add text to the image as if the text is a VOI; annotations are savable when the image is saved in the MIPAV XML format. These annotations are not saved when saving other in other image formats

• Resizing of the surface & volume renderer GUI now better displays on different resolution screens
• Upgrades to documentation
• Changes to file I/O:
  • DICOM changes:
    • Multiframe DICOM images can now be anonymized
    • Sequence tags are being saved properly (again)
  • MRC writer properly sets extents
  • TIFF color maps now have a proper ceiling
• Fixes to BSE algorithm:
  • Scripting now works in all cases
  • Brain volume now more accurately calculated
• Upgraded the installer to use InstallAnywhere version 6.1; this means that MIPAV now runs faster, since the the "-server" command switch is now supported

• Additional upgrades to the brain extraction algorithm (BSE), faster and more robust
• Histogram summary utility has been added
• Upgrades to the GUI, in particular, to the button icons
• Removed redundant logging function tab from output window. Scripts and recording history remain
• Fixed bug introduced in the last version that caused utility -> rotate X axis +/- 90 to fail

• Brain extraction algorithm has had significant upgrades. It now produces results similar to BSE from UCLA.
• BET was modified to better estimate the center of the initial centroid.
• Fixed FRET and FRAP bugs that had a problem processing images with only blue and green color channels.
• Changes to DICOM functionality
  • Resolved:Reading & storage of slice-spacing and slice-thickness problem resolved
  • Resolved:Sequence information saved correctly
  • Private tag display has improved
• Made the Analyze file reader more robust. Now able to read mages from the Internet Brain Segmentation Repository
• Fuzzy C-means classifier now outputs the volume for each class found.
• Fixed bug when saving images from a script
• Documentation updates, including major revision of the section on DICOM
• Fixed bug which caused painting (for VOI interest delineation) to be inconsistent between 2D planar view and triplanar view
• Changes to Help -> Program Options
  • "help" button to provide context-sensitive assistance
  • added parameter to provide a global option to retain, as default, the inputted parameters in dialogs
  • added parameter to provide an option to display the paint toolbar as a default setting

• Improved robustness in handling the ICS format
• Enhanced subsample utility to handle 2D, 3D and 2.5D (3D-by slices)
• Volume to slices fixed
• Removed tetrahedron from surface extraction; we now only perform cube extraction
• Utility to extract slices or volumes into separate frames
• Fixed: Now prompts for image type when an image does not have a filename extension; previous version failed to prompt for this information
• Fixed: Switching from the volume view to the slice-view in the rendering window no longer turns off the slices

• Improved LSM reader to properly interpret color order
• Fixed: the typo in ViewJComponentColocalizationRegression for green and blue coloring
• Changes to Morphology
  • Improved ultimate erode for 2D images
  • Improved particle analysis for 2D images
• Improved DICOM to XML converter
• Ability to save surfaces in VRML format has returned to Surface viewer GUI
• Switching from a volume rendered view back to the three-plane surface-rendered view causes all three planes to be switched "off" -- the slice control checkboxes must be selected back to "on" to redisplay the slice planes.

• Fixed: XML image reader now properly reads MIPAV XML format color images which do not reference any VOIs.
• A link to the Uninstaller is now placed in the same location as the shortcut to the program itself to aid the user when installing a newer version

• Oops: A feature added to make color XML reference VOIs causes those which don't to not load
• File Reader improvements
  • Improved ICS file reader
  • More robust MINC v 1.0 reader
• Concatonation Utility has been changed so that it retains DICOM and XML header information in the concatonated image
• Laplacian and Non-maximum supression edge detection now correct zero-crossing identification
• VOI are painted so that the top-most VOI is painted last (and therefore on top)
• More information has been added to algorithms section of the documentation, notably, FRET algorithm is now documented
• Fixed: Previous version did not allow selection of the Optimized Automatic Registration (see Algorithms -> Registration -> Optimized automatic registration 2.5D)
• Some of the algorithms now have the entered values saved as defaults; the number of algorithms supporting this behaviour will increase with future versions
• Fixed: Working images during FRET algorithm are now properly cleaned up
• It is now possible to run FRET algorithms on two images in the same frame
• The image browser (File -> Image browser) allows the user to open the selected images in one frame or each image in its own frame
• Correction made to saving surfaces in scanner coordinate system
• Now able to remove objects outside a user specified size range (see: Algorithms -> Morphology -> IDobjects)
• Bugfix to the subsample utility (Utilities -> Subsample) for subsampling 2.5D images

• Ability to convert 4D to 3D (see Utilities -> Convert 4D to 3D) has been added
• Updated documentation for scripting
• Added "help" button for context-sensitive help
• Updated image.xsd so it now stores references to surface data
• Further improvements to the Surface and Volume renderer
• Fixed: Marker parameter updated to AFNI format
• Fixed: XML Info editor

• Any image attributes can overlay the image, regardless of type
• Fixed:DICOM reader now reads images with sequence tags of unknown length when item tags of known length are present.
• Fixed:Pixel Padding is again used correctly
• Added two new algorithms for threshholding: OTSU and Maximum Entropy. They are accessible from the Algorithm -> Threshold dialog as well as buttons in the histogram window
• Image browser can now open multiple images as a part of the same image
• DICOM Browser
  • Handles more image variations because of the DICOM reader fixes
  • Can automatically read dcm, ima and files with names derived from a UID
  • Reverts to default mouse icon when done (after failing) instead of still looking "busy"
• Added a screen-grab icon to the main frame
• Surface and Volume renderer interface has been through an extensive update. A number of functions have been merged as has the button on the main frame

• Buffering end-slices now allows several algorithms (Median and Mode) to act on the end-slices rather than ignoring any action.
• Speed increase using Multi-spectral Fuzzy C-Means
• Updates to the contextual Help file
• Name changes to assist the way the Script Parser works; the user who writes Plugins should consult the API document to see the new names
• Known issue:The DICOM reader does not appear to read Sequence tags which do not define a known length, but use item tags which do

• Added the ability to allow the user to identify which DICOM tags are to be in the DICOM overlay
• Saving to MIPAV's xml file format now reads and writes the image's transformation matrix
• Animate player bug has been fixed so that the user can save in AVI
• Improvements to the Brain Surface Extractor so that it now uses far less memory; there is now a help available for it
• Additionally, added help buttons to: Cogerence Enhancement Nonlinear Diffusion and Regularized Isotropic Nonlinear Diffusion Filter
• Added morphological operations to process 2.5D (multislice 3D) images
  • Erode
  • Dilate
  • Open
  • Close
• The java switch "-server" has been added to the InstallAnywhere startup. This is a responce to the benchmarking paper Java Faster than C++ paper, noting the section "Using the Server JVM". We noticed that the time required for an algorithm to complete would decrease anywhere from 5% to 50%.
• Installation under Macintosh OS 10 is now much easier; The end-user must still remember where Java WebServices is installed, but the installer now asks for the location and modifies the startup file. The user is no longer required to modify files by hand

• Added the algorithm Face Anonymization to modify the facial structure in MRI and CT datasets so that the patient's face is unrecognizable during volume or surface renderering
• Added an implementation of the Brain Surface Extractor (BSE), accessable from the menu: Algorithm -> Evolve Surface -> Extract Brain Surface (BSE)
• DICOM browser enhancements
• DICOM tag (0020,0037), Image Orientation, which encodes the transformation matrix, that can be used to transform the image to an axial orientation, is stored in the image's associated transformation matrix
• Now loads photobleach ROIs from the Zeiss (LSM) file format
• Dual-triplanar upgraded to allow landmark placement for thin-plate spline or least squares registration
• Colocalization bug when second iteration option is chosen has been fixed
• Levelset VOI is more robust and more likely to produce a reasonable boundary
• Bug fix to Algorithms -> Edge Detection -> Zero-Crossings of the Laplacian
• 3D Affine Registration (OAR) now supports the ability to define the rotational search-space for each axis (x, y and z); in addition, the possibility of finding a solution outside the search range has been reduced
• An automatic, non-linear, b-spline registration algorithm (Algorithms -> Registration -> Nonlinear B-Spline Automatic Registration) has been added
• An output option called "Decompose" has been added to Image -> Attributes -> Edit Attributes under the Transformation Matrix tab; this option decomposes the transformation matrix into rotations, translation and scale and is displayed in the Global Data tab of the Output frame

• AVI with audio can now be read, although the audio is stripped away and ignored
• Improved Volume renderer: volumes displayed are now more crisp and less fuzzy
• Surface renderer allows 3-slider movement of displayed intersecting 3-plane slices
• Can now save DICOM images with sequence tags

• Triplanar Surface viewer updates
• Surface renderer interface improvement
• Color matching
• Bugfix to FRAP format
• Bugfix to colocalization
• DICOM reader should now properly read in images with Sequence tags; Known issues: DICOM images with sequence tags are not yet correctly written out to file; tags held within a sequence are not yet displayed in-order

• Updates to the AVI reader, so it now reads both 8 bit and 16 bit Windows AVI files.
• Adding a second image to an already open image frame now converts the units, down to differences of 10**-6
• Bugfix to FRAP format
• AFNI now writes markers
• Seperable Convolver is now faster (~30%)
• Interactive level set produces smoother boundaries
• Some DICOM fixes:
  • DICOM receiver start-up when MIPAV starts now follows preferences
  • DICOM tag (0000,0070), Command Priority, is being properly sent for C- commnands
• Gaussian Blur now supports 4D images
• There is a change to the XML Image format, to permit logging changes made to image files (ie., logging)
• 3-D texture mapped volume rendering is greatly improved.

• MIPAV can now be called on the command line. Call on the command line with the option -h to view the command help dialog box
• NIFTI file support is now included
• AVI updated to read MS-CRAM format
• Convert Type can now act on individual slices
• DICOM unsigned short type images now save correctly [note: DICOM images with SeQuence data are still not saved properly; this should be corrected in the next version]
• Now includes a volume renderer (the Raycast Renderer)
• Improvements to the Surface Renderer
• Surface and three-plane views can now be viewed simultaneously with the Volume Tri-planar View Tool

• updates to Colocalization
• Updates to FRAP tools
• AVI updates
• Load Image changes

No changes listed.

• Faster DICOM file read
• Faster Fuzzy CMeans
• Capture screens fused image into single RGB image
• TSP uses less memory and is faster
• updated Macintosh installation instructions are not yet complete.
• Includes a utility to update MIPAV XML file format information to the most recent revision

• Marching cubes surface extraction has been added
• Colocalization
• Faster
• More options
• Update documentation
• Frap Improvements
• Better curve fitting
• Minor improvements to GUI
• Algorithm to quantify segmentation results by comparing segmentation to user-provided "gold standard". Produces results for:
  • False negative volume fraction
  • False positive volume fraction
  • True Positive volume fraction
• Reads point VOIs as spheres into volume renderer
• Minor improvements/ bug fixes to file formats:
  • VRML
  • ICS
  • LSM (Zeiss)
• Option added to save MIPAV formatted XML files in zipped format
• Updated documentation and help
• Added API to web page
• 2.5D Registration now supports 2 Degrees of Freedom (just translations in x and y dimensions).
• Surface renderer now supports view-aligned 3D texture mapping.
• Improve scripting with VOI
• Transform algorithm now allows the user to indicate whether the image origin should also be transformed.

No changes listed.

• API organization glitches have been worked out.

• Removed API organization until the glitches can be worked out.

• Updated contact information
• VOI Bug-fixes:
  • VOI selection and movement across different slices is now consistent
  • Grouped VOI labels are now changed to represent the new group
• A change in the way Macintosh installation checks for Java Virtual Machine versions
• Test build to test plugin creation
• More adjustments to scripting
• Improvements to co-localization
  • much faster
  • Cleaner interface
  • Free-form
• Faster and cleaner surface renderer
• Utilities now have complete documentation

• FRAP Analysis improvements
• VOI Improvements:
  • Colour indicator on tool-bar
  • Contour numbers
• File format improvements:
  • Updates Zeiss reader to conform to Zeiss 3.2 Specification.
  • Updated ICS reader to automatically unzip gzipped images
• Bug fixes to VOI statistics generator
• Major improvements to scripting