What's New

Previous changes to MIPAV

4.1.3 (10/15/2008)

• File handling
  • Added automatic detection of DICOM ver. 2 files without the .dcm extension.
  • Eliminated some memory leaks in the DICOM reader and writer.
• Algorithms and utilities
  • Added Morphological algorithm support for processing Byte and Short images that have no negative values.
  • Fixed an error that sometimes occurred while running the BET algorithm.
• VOIs and Paint
  • When commiting masks for a 4D image, the multipaint dialog has radio options for commiting masks as 3D or 4D; for regular painting in the 2D view and in Tri-planar image, a dialog pops up asking if masks are to be commited in 3D or 4D when trying to commit paint to mask.
  • Fixed a problem with the Protractor tool in the Tri-planar view.
• Help updates and additions
  • Added help topics on the Hough circle, ellipse, line and parabola algorithms.
• Miscellaneous
  • Fixed a problem setting the output directory of the generated file when performing a screen capture.
  • Fixed support for printing the contents of the Output window.

4.1.2 (09/12/2008)

• Fixed a problem with the MIPAV installer which caused the 4.1.1 release for Windows-amd64 systems to fail to start up.
• File handling
  • Fixed an issue with decoding 24-bit CVID AVI files.
  • Added support for black and white CVID AVI files.
• Algorithms and utilities
  • Fixed a matrix-copying issue when running algorithms and utilities on DICOM images.
• VOIs and Paint
  • More improvements to VOI text annotation.
• Image views and visualization
  • Fixed a problem with the GPU renderer on Macintosh systems.
• Help updates and additions
  • The MIPAV Help system has been changed significantly. Each help topic now contains information on using the component it is associated with and a link to a page on the MIPAV website which has background information for that algorithm or utility. This has significantly reduced the amount of disk space taken up by the MIPAV Help system.
• Miscellaneous
  • Fixed a problem which prevented the command line argument usage window from appearing when the -hide command was not used.

4.1.1 (09/08/2008)

• File handling
  • Cleaned up memory usage of a number of file handlers.
  • Added 8-bit grayscale support to JIMI reader (JPEG, etc).
  • Added support for saving Analyze float images to DICOM.
  • Fixed an issue with capital letters in file extensions.
  • PAR/REC files may now be opened by selecting either the .par or .rec file.
  • Improved SPM file format detection.
  • Fixed a problem with reading COR files.
  • Fixed an issue with the VOI file filter.
  • Changed the saving of 3D DICOM datasets to be done on a slice-by-slice basis to reduce memory usage and prevent problems with large datasets.
  • Fixed some issues with MINC2-HDF orientations.
  • Added AVI decoder support for 24-bits-per-pixel CVID files.
• Algorithms and utilities
  • Fixed a number of minor bugs:
    • Regularized isotropic diffusion
    • Gradient magnitude
    • Gaussian blur
    • Center of mass
    • Watershed
    • Edge lapacian
    • Image calculator
    • Registration patient position
    • Registration B-spline
    • Registration mosaic
    • Registration OAR 2.5D
    • Registration TSOAR
    • Transform
    • Subsample
    • Pad
  • Added the display of the standard deviation when the Image calculator and Bulk image calculator are run.
  • Added Poisson noise to the Noise generation utility.
  • Added a utility to swap the 1st and 4th dimensions of a 4D image.
  • Added a new utility to reorient (and optionally resample) an image (contributed by Pilou Bazin).
• VOIs and Paint
  • Corrected some minor issues with the Multi-paint tools.
  • Improved memory management while painting, reducing memory creep and removing a garbage collection call performed on 64-bit JVMs.
  • Livewire VOI now works with color images.
  • Fixed a Power paint dialog bug.
  • Fixed a problem with creating custom brushes.
  • Changed paint behavior so that when the user paints in the main image frame, the paint in the Tri-planar frame is only updated on mouse release.
  • Fixed a race condition when switching paint colors in the Multi-paint dialog.
  • Fixed some issues with VOI annotations.
  • Improved how backing up and reverting to the paint bitmask backup is performed. This significantly improved paint performance with large images on initial mouse press and when undo-ing an action.
  • Converting a VOI in a 4D dataset to a mask image now produces a 4D volume with the VOI converted on all time slices.
• Image views and visualization
  • Improved the surface decimation algorithm.
  • Added PLY surface format support.
  • Added the ability to save the current camera and object parameters in the GPU Volume renderer and restore them again later.
  • Improved surface extraction algorithms to automactially reduce surface complexity.
• Scripting
  • Fixed Transform scripting bug when resampling.
  • Fixed a scripting issue with the Optimized automatic registration algorithms.
  • A number of algorithms were being run in a separate thread during script execution (FFT, std dev thresholding, registration OAR 2.5D and 3.5D, background distance map, evaluate mask segmentation, evaluate segmentation, remove t-slices).
• Help updates and additions
  • Muscle segmentation plug-in.
  • Conformal mapping algorithms.
  • DICOM query dialog.
  • DICOM images section.
  • Wavelet thresholding.
  • LUT for two images (A and B).
  • Filters (frequency).
  • Wavelet BLS GSM.
  • Talairach transform
  • Modify graph
  • Paint grow
  • 2D B-spline registration
  • Mosaic registration
  • Scripting
• Miscellaneous
  • Added menu items Open graph to same frame
  • MIPAV classes no longer use Java3D vecmath classes. Instead WildMagic vector and matrix classes are now used. Usage of Jama classes has been refactored and the location of the code within the MIPAV classpath has been changed. MIPAV Vector*, Color* and Point* classes have all been removed.
  • Added -outputDir command line option for selection of the directory where files written out to disk by MIPAV should be located (to be used with scripting).
  • Changed -dir command line option to -inputDir.
  • Fixed a problem where an error dialog would sometimes pop-up when running MIPAV with the -hide command line option.

4.1.0 (06/13/2008)

• File handling
  • Gzipped archives (containing a single file in a format supported by MIPAV) can now be automatically un-archived and opened in MIPAV.
  • Improved the processing of determining the file format of files with an unknown or non-existent extension.
  • Fixed a problem where .tiff files would not show up in the Image browser when the TIFF file filter was selected.
  • New file formats supported:
    • BFLOAT
    • LIFF
    • Minc2
    • STL surface format (.stla and .stlb)
    • VTK surface format
  • File formats with bug fixes or improvements:
    • Analyze
    • Biorad
    • DICOM (UT supported as explicit VR with 32-bit length; reading of critical tags that were incorrectly written)
    • DM3
    • ICS
    • Minc (slice thickness now saved to the acquisition -- slice_thickness attribute)
    • OSM
    • PARREC
    • TIFF
• Algorithms
  • Added automatic parsing of ITK filter interfaces for access from the Algorithms menu (available only on 32-bit Windows systems, by default).
  • Image calculator (added color support)
  • Image math (added color support)
  • Match for reference
  • Match images
  • Maximum intensity projection (added color support)
  • Transform (adjusts units of measure of input image to match reference image)
  • The Threshold and dual threshold tools now output unsigned byte instead of short masks.
  • Improved the multi-threaded image convolution support.
  • Parallelized the Optimized automatic registration algorithm.
  • Integrated the Talairach transform plugin from JHU Medic into MIPAV.
• Utilities
  • Moved Center of mass from the Algorithms menu to the Utilities menu.
  • Improved the Center of mass output sent to the Output window's data tab.
  • Fixed the way that the Rotate utilities handled setting the VR of DICOM image tags.
• VOIs and Paint
  • Fixed a problem with cloning some VOIs.
  • Fixed some issues with the Livewire VOI tool.
• Image views & visualization
  • Parallelized the Raycast volume renderer.
  • Many improvements have been made to the GPU-based volume renderer.
  • Multipaint dialog improvements -- auto-save for multiple masks and keyboard shortcuts that work with the triplanar view.
  • Changed the paint brush sizing in the triplanar view to be consistent regardless of the image resolution.
  • Added Paint -> Unsigned byte mask conversion tool.
• Scripting
  • The Transform algorithm now saves the relative path to the transformation matrix file in its script action line, if a file is selected in the dialog.
  • Added -dir option for setting the default image directory when running scripts from the command line.
• Miscellaneous
  • The MIPAV installer now tries to correct the permissions of file containing memory limit.
  • Added a checkbox in the MIPAV options dialog for the enabling/disabling of the parallelization of algorithms.
  • A Capture screen memory leak was fixed.
  • Many DTI algorithm and visualization improvements have been added.
  • Moved the keyboard shortcut file (accessory.dirs) from the user.home directory to user.home/mipav.

4.0.3 (02/29/2008)

• File handling
  • AVI transcoding bug fixed.
  • Added support for many new variations of the TIFF format.
  • Fixed some minor issues with the Interfile reader.
  • Fixed some minor issues in the Afni reader.
  • Fixed some minor issues in the Analyze reader.
  • Solved a problem in MIPAV's support of NIFTI multifile datasets.
  • Added XFM matrix file format support (McGill transforms).
  • Fixed problem storing very large float or double values into a unsigned integer image buffer.
  • Fixed NRRD reader progress bar.
  • The user can now select DICOM tags to save from the Image header dialog (this action is scriptable).
  • Improved dialog for selection of tags to convert from DICOM to XML.
  • Fixed a problem encountered reading DICOM files with malformed slice thickness (0018,0050) or slice spacing (0018,0088) tags.
  • Solved problem reading reading DICOM CT images stored as unsigned short on disk with negative rescaling.
  • Fixed NRRD matrix and origin orientation problem.
  • Added option in the MIPAV options to always open img/hdr files as either Analyze/NIFTI/Interfile or to force MIPAV to always prompt the user. This change may cause some temporary problems when scripting the saving of files to these formats with the -hide option.
  • Modified Par/Rec reader to handle new version of the header file.
• Algorithms
  • Parallelization of Optimized automatic registration, non-linear registration (b-spline and least squares), FFT, and separable convolver-based algorithms to take full advantage of multi-processor and multi-core systems.
  • Fixed a problem with the Transform algorithm.
  • Fixed bug in FFT algorithm.
  • Added beta version of auto-exposure of Insight Toolkit (ITK) filters from within MIPAV.
• Utilities
  • Fixed the Image calculator utility difference and average functions for complex images.
  • Added an Image calculator - bulk images utility to perform calculations on multiple open images.
  • Added a utility to calculate an image's center of mass.
• VOIs
  • Added Coefficient of skewness and Coefficient of kurtosis to VOI statistics/properties.
  • Center of mass has been renamed Geometric center in the VOI statistics/properties.
  • Fixed display of scanner coordinates for VOI points in the VOI statistics/properties output.
  • Fixed problem in Rectangle VOI.
  • Added new button to open VOI properties dialog.
• Image views & visualization
  • GPU renderer (beta) improvements:
    • Added support for GLSL programmable shaders.
    • Ported volume renderer slice view.
    • Fixed miscellaneous bugs.
    • Added volume sculpting support.
    • Added triangular surface mesh support.
    • Improved clipping planes.
    • Added ability to paint on surface meshes.
  • Added new LUT color scheme presets.
• Scripting
  • Added support for graphically selecting transformation matrix files for use when scripting the Transform algorithm (Contributed by Pilou Basin).
• Miscellaneous
  • MIPAV now consistently displays slice positions in a zero-based format.
  • Plugins can now be run without the rest of the MIPAV interface appearing by using the -p PlugInName command line option with the -hide option.
  • Added the following help topics:
    • Morphological filter
    • Skeletonize 3D
    • Surface plotter
    • Barrel/pincushion distortion correction
    • Cumulative histogram
    • Image calculator - bulk images
    • Creating a self-contained plug-in frame
    • Display pixel similarity cost function

4.0.2 (11/15/2007)

• File handling
  • Added support for writing NRRD files.
  • Resolved a problem with some 2D Nifti files.
  • Fixed writing of image matrix to MIPAV XML for 4D+ datasets.
  • Fixed reading of some (uncompressed, ISFT, LIST, IV32, IV41) AVI files.
  • Afni reader now allows the time dim to be set to 1.
• Algorithms
  • Fixed Transform algorithm handling of VOIs when 2.5D processing is performed.
  • Minor bug fixes included for a number of algorithms:
    • Extract brain (BET)
    • Registration mosaic
    • Registration OAR 3D, 3.5D, 4D
• Utilities
  • Merged Pad and Add image margins utilties
  • Minor bug fixes included for a number of utilities:
    • Change type
    • Clone
    • Crop
    • Depth flip
    • Image calculator
    • Image math
    • Maximum intensity projection (MIP)
    • Noise
    • Quantify mask
    • Randomize slice order
    • Remove slices
    • Replace removed slices
• VOIs
  • Fixed a minor bug in VOI histogram when there is no VOI contour present.
  • The Livewire dialog now maps the Enter key to the OK button.
• Image views & visualization
  • More Diffusion tensor tool updates.
  • Continued improvements to the WildMagic GPU-based renderer.
• Scripting
  • Fixed recording and playback of the 'Invert matrix' flag in the Transform dialog.
• Miscellaneous
  • Fixed image min/max calculation for boolean images.
  • Added the following help topics:
    • Background distance map
    • Close
    • Delete objects
    • Dilate
    • Distance map
    • Edge laplacian
    • Edge NM suppression
    • Erode
    • Evaluate mask segmentation
    • Evaluate segmentation
    • Fill objects
    • Find edges
    • Histogram summary
    • ID objects
    • Multi-paint
    • Open
    • Particle analysis
    • Power paint
    • Skeletonize
    • Standard deviation threshold
    • Ultimate erode

4.0.1 (10/12/2007)

• File handling
  • Fixed Image-offset tag value in MIPAV XML files saved from some other formats.
  • Fixed the XML image header file name set for new images created as a result of some algorithms.
  • Fixed an error which would occur when writing Dicom images with some types of sequence tags to the MIPAV XML format.
  • Found and resolved a bug in writing some datasets to the Nifti (.nii) format.
  • Modified the Minc reader to support 4D volumes.
  • An optional tag indicating the dataset slice thickness has been added to the MIPAV XML file format specification.
  • Fixed a problem with handling some version number strings in the NRRD file reader.
  • The NRRD file format has been added to the Medical file type filter used in the Open and Save image dialogs.
• Algorithms
  • Fixed VOI region processing in multiple algorithms:
    • Find edges
    • Particle analysis
    • Thin
    • Prune
    • Ultimate erode
    • Laplacian
  • Removed 2.5D processing option from Particle analysis algorithm dialog.
  • The Extract brain (BET) algorithm now defaults the 'Axial brain orientation' parameter to selected when using an Axial image.
  • Fixed some data value wrap-around issues when running the Laplacian algorithm. New images generated are now always stored in a float datatype. When replacing the source image, the result data values are scaled to fit within the source image datatype (when necessary).
  • When running the Frequency filter algorithm with the replace source image option, the image datatype is now forced to float.
  • Fixed a bug in the Homomorphic frequency filter.
  • When running the Anisotropic diffusion algorithm with the replace source image option, the result data is rescaled if it does not fit within the source image data range.
  • Fixed 2.5D VOI region processing for some combinations of images and parameters in the Laplacian algorithm.
  • Improved the Median filter algorithm dialog and made traditional filtering the default choice.
  • Fixed the AHE local algorithm progress bar for 2D color images.
  • Fixed the display of the wavelet image under certain conditions in the Wavelet threshold algorithm.
  • Removed duplicate data output by the Colocalization regression algorithm.
  • Fixed a small bug in the subsampling routine of the Entropy minimization algorithm.
  • When running the Principal components algorithm, the filtered and average destination image values are rescaled if they exceed the image data type range.
  • Fixed a problem in the Maximum likelihood iterated blind deconvolution algorithm resampling routine.
  • Fixed a bug in the processing of 2D images with the Two MRI images signal-to-noise ratio algorithm.
  • The Subsample algorithm now copies over VOIs from the original image to the result volume.
  • Fixed a few small interface issues in the Transform algorithm dialog.
  • Fixed the behavior of 2D and 3D B-Spline registration progess bars.
  • Constrained optimized automatic registration is now disabled for 2D images.
• Utilities
  • Correct image spacing now operates on all image formats, not just MIPAV XML. It also handles situations where correction is not needed more gracefully.
• VOIs
  • Added a VOI splitter tool, which allows the user to divide one VOI into two.
  • VOI statistic values are now saved in the Parameter set portion of the header of MIPAV XML images.
  • Added sum intensities to the list of available VOI statistics in the VOI properties dialog and VOI statistics generator.
• Paint
  • The buttons to Hide masks and paint in the Multipaint dialog now update the Tri-Planar view as well.
  • Added the ability to Lock/Unlock all masks in the Multipaint dialog.
  • A number of Power paint dialog upgrades have been made:
    • Support for color images has been added.
    • The Threshold GUI has been changed to spinners.
    • Added the ability to use the thresholds during paint growing and dilation.
• Image views & visualization
  • Added support for reading and writing of VTK XML surface files (*.vtp).
  • Added the ability to adjust the raytracing step size in the GPU-based volume renderer.
• Help topic updates and additions
  • Advanced paint
  • Edge dection
  • Histogram tools
  • Morphology
  • Segmentation
  • Utilities
• Miscellaneous
  • Added tools for DTI image segmentation and visualization.
  • Masks created and placed into the ImageB slot are now named according to the current ImageA volume.
  • The Insight Toolkit Kit (ITK) dlls distributed with the 32-bit Windows MIPAV installers have been updated to version 3.2.0.

4.0.0 (09/07/2007)

• File handling
  • Fixed problem reading in multiple matrices in MIPAV's XML image file format.
  • When converting from Minc to DICOM, we now ignore Sequence tags stored within the Minc header since they are generally not stored in a consistent format.
  • Improved the memory management of the Nifti file reader and writer.
  • Fixed the saving of orientation and other header information when converting non-Nifti files to the Nifti file format.
  • Fixed a bug in data type handling for some DICOM files.
  • Fixed a problem in the PAR/REC file reader.
  • Fixed a bug in the Afni file reader.
  • Fixed the image offset value when saving XML files from other image file formats.
  • Fixed a bug reading in encapsulated DICOM files.
• Algorithms
  • Fixed a memory leak in the Colocalization EM algorithm.
  • Added option to insert padding into an image before running the Subsample algorithm to make the image extents divisible by the sub-sampling factor.
  • The Histogram summary now allows the user to specify the summary minimum and maximum.
  • Fixed a bug in the BET algorithm.
  • Fixed the Separable edge laplacian algorithm progess bar for 2D images.
  • Fixed the Auto covariance progress bar.
  • Fixed the Subsample dialog's expected extents labels for 2D images.
  • Fixed a problem in the Subsample algorithm's memory management.
  • Removed the bandpass and bandstop options from the Frequency filter algorithm for Gaussian filters.
  • Solved a progress bar problem for the Adaptive path smooth algorithm.
  • Disabled Boundary attenuation algorithm for 2D images.
  • Fixed a memory management problem in the Coherence enhancing diffusion algorithm.
  • Added a kernel error check for the separable Gradient magnitude algorithm.
  • Fixed a bug in processing a VOI region with the Gradient magnitude algorithm.
  • Fixed a bug in processing a VOI region with the Erode algorithm.
  • Fixed a bug in processing a VOI region with the Distance map and Background distance map algorithms.
• Utilities
  • Fixed Crop utility when Replace image was selected. Also fixed a memory issue when cropping DICOM images. Fixed a problem with a warning dialog which popped up when no VOIs were selected.
  • Fixed a bug in the Pad utility's handling of 3D RGB images when Replace image was selected.
  • Fixed a crash when attempting to run the Rotate utility on 2D, non-DICOM images.
  • Added the option to threshold an image before generating its Maximum intensity projection using the MIP utility.
  • The Flip utility no longer displays the option to flip 2D images along the Z axis.
  • Fixed bounds checking problem in RGB concatenation utility.
  • The Quantify using mask utility can now be run on RGB images. It also outputs the mean and standard deviation for grayscale or RGB images. The mask can be loaded from a file or from an image frame.
• VOIs
  • Improved the progress bar of the Rubberband livewire VOI tool.
  • Fixed a bug in the Smooth VOI with the Replace original contour option selected.
  • When VOI graphs are generated, the mean and standard deviation is now output to the data window.
• Image views & visualization
  • Added a new hardware-shader-based volume rendering system. It is based on a port of the WildMagic libraries to Java. It currently requires a modern Nvidia graphics card and is a beta release.
  • Fixed initial zoom of Tri-planar view on some datasets.
  • Fixed a problem with the magnification when the zoom is set below 1x.
  • Added a new XML surface file format that references a .sur file, which contains the surface mesh data (resulting in faster surface loading).
  • Improved speed of Talairach Tri-planar view.
  • Added support for the .vtk legacy surface file format.
  • Fixed a bug in the saving of VRML and WRL surface file formats.
  • Added the ability to view surfaces within the volume renderer without viewing an image volume.
  • Fixed a number of minor bugs in the Java3D volume renderer.
• Scripting
  • Fixed a problem when executing a script with CloseFrame actions from the Run script dialog.
• Painting
  • The Power paint tools are now disabled for 2D images.
  • Extracting a paint mask to a new image now uses the correct paint intensity.
  • Fixed problem when collapsing paint and mask layers for RGB images in the Multi-paint dialog.
  • Fixed an error in the Multi-paint dialog when a RGB imageB is present.
  • The Paint calculator button now calculates total intensity, mean intensity and standard deviation of the painted region.
• Miscellaneous
  • Added installer support for 64-bit Windows systems.
  • MIPAV installers for Windows and Linux systems now include Java virtual machine 1.6.0_02, JMF 2.1.1e, Java3D 1.5.1, Jogl 1.1.0 and Nvidia Cg Toolkit 1.5.
  • Added BIRN data provenance 2.0 support. This information may be tracked globally and for each image. The provenance data can then be saved to an xml format along side an image file (with an .xmp file extension). It records algorithms and utilities applied to an image volume (i.e., the image's history) and information about the version of MIPAV used.
  • Many improvements and additions have been made to the MIPAV help. A few of the changes include:
    • Added Talairach transform topic.
    • Added MIP utility topic.
    • Updated Quick start chapter.
    • Updated Plugins section.
    • Updated Dicom browser topic.
    • Updated Segmentation topic.
  • Fixed a problem with the image frame resize handling on some systems.
  • Fixed some minor problems in the uniform and gaussian random number generators.
  • Added some SRB security measures:
    • 10 SRB login failure lockout.
    • 30 minute SRB inactivity auto-logout.
    • NDAR privacy notice on successful SRB login.
  • Removed BIRN Xcede-related features.
  • Changed PlugInAlgorithm and PlugInView interfaces to remove the ViewUserInterface parameters from their run() methods.

3.1.6 (06/20/2007)

• File handling
  • PAR/REC save support added.
  • Fixed the DICOM directory anonymizer's handling of directories which contain some non-dicom files.
  • DICOM files are now saved with explicit VRs for the 0002 tag group.
  • The DICOM receiver also attaches 0002 group tags with explicit VRs to the files it receives.
  • The DICOM sender now allows the user to select multiple files to send, skipping any that are not DICOM files.
  • When saving an image as a DICOM file, the Patient age tag (0010,1010) no longer needs to be entered with leading zeros into the Save dicom dialog.
  • Fixed the reading of DICOM images that do not have a DICM preamble.
  • Fixed the saving of individual 2D slices from a 3D XML image.
  • Fixed a problem saving Analyze files with file names longer than 18 characters.
• Algorithms
  • Added Barrel distortion correction algorithm.
  • Fixed a bug in the Fuzzy C means algorithm.
  • Fixed a problem in the Median filter that caused it to ignore its standard deviation parameter.
  • The Transformation dialog now allows for both a transformation and a resampling to be performed at the same time.
• Utilities
  • Added a utility to add padding to an image.
  • Cropping an image without creating a new image now properly updates the image matrices.
  • Help topics have been added for many algorithms.
  • The Quantification utility now uses the individual slice resolutions to make volume calculations.
• VOIs
  • Fixed copy/paste of VOIs.
  • Fixed handling of poly-slice line selection/deselection.
  • Fixed a problem loading some scanner coordinate VOIs.
• Image views & visualization
  • Fixed issues with saving/loading XML surface mesh files in the Volume renderer.
  • The Extract surface algorithm now can produce an XML surface mesh file.
• Scripting
  • Fixed an error in the scripting of the Median filter algorithm.
• Miscellaneous
  • Fixed a problem opening the Multi-paint dialog or creating a new mask with some DICOM images.
  • Fixed a bug where the paint cursor was not getting changed when an image B was open in the Tri-planar view.

3.1.5 (05/31/2007)

• MIPAV 3.1.5 fixes a major file read/write bug in the 3.1.4 release of MIPAV. See the cumulative listing of changes for the many enhancements and changes which were included in MIPAV 3.1.4.
• Fixed a major series of bugs in the handling of dialogs which pop up when the user reads or writes some file types in version 3.1.4. These bugs prevented some file types from being read or saved properly.
• Added a new toolbar icon to link all images with dimensions similar to the current image frame. When the slice of this image is changed, all of the similar images also change their displayed slice.
• When the Multi-paint dialog changes the current paint color, the paint cursor now also changes color to match it.

3.1.4 (05/29/2007)

• File handling
  • Major refactoring of the DICOM reader and the manner in which DICOM tags are stored. This has resulted in a doubling of the read speed and a halving of the memory required for many DICOM datasets.
  • Added sorting to the file listing in the Open image sequence dialog.
  • Fixed a bug in the PAR/REC reader when the directory containing the files included the strings 'par' or 'rec'.
  • Fixed some issues with NIFTI orientations and the orientation of 2D NIFTI files.
  • Corrected the image file names stored when a GE Genesis 5x, GE Signa 4x and Magnetom Vision dataset is read in.
  • Multi-file datasets with very large numbers (e.g., a dataset UID) in their file names can now be opened. The number is truncated so that it fits within a long and can be compared to the numbers found in other file names.
  • Fixed a problem in reading in multi-file Analyze images.
  • Fixed a bug reading some big endian DICOM files.
• Algorithms
  • Fixed the progress bar in the Unsharp mask algorithm.
  • Updated the 'Registration: Manual 2D Series' help topic.
  • Updated the Brain surface extractor and Brain extraction tool help sections.
  • Maximum likelihood iterated blind deconvolution now resamples the input image to a power of 2 automatically and fixed the algorithm's progress bar.
  • Updated the Maximum likelihood iterated blind deconvolution help section.
  • Added help topics for the 'Talairach transform' and 'FANTASM' dialog boxes.
  • Modified Particle analysis dialog to allow for selection of kernels for the close operation.
  • The Threshold algorithm now defaults the threshold min and max to the min and max of the image.
  • Updated the Threshold algorithm help topic.
• Utilities
  • Mask to paint conversion now operates properly on a RGB image.
  • Added a new help section for the Maximum intensity projection utility.
  • Added the ability to force the result image to contain float values in the Image math dialog.
  • Added a new utility which converts a 4D image with one, two, or three volumes into a RGB image (1st volume -> Red, ...).
  • Quantify mask now checks to see if the input image is a mask image by requiring the difference between its max and min to be less than 100.
  • Added help topic for the Image calculator utility.
• VOIs
  • Added an option in Help -> MIPAV options to save VOIs in either file coordinates (the old method) or in Left-Posterior-Superior coordinates (the new method).
  • An option has been added to the Tri-planar view which forces the Protractor VOI to snap to increments of 90 degree angles when it is released.
• Image views & visualization
  • Resolved an error in the Tri-planar view when the Paint grow dialog was closed and the used clicked in the image.
  • Added the option to extend the Tri-planar view crosshairs so that they intersect.
  • Added the option to link the Tri-planar crosshairs to the original image, so that scrolling through the image slices in the Tri-planar causes the original image frame to do the same.
  • Fixed the performance of the Lightbox view.
• Scripting
  • A script action with no images and no VOIs is now handled correctly.
  • When using raw images in a script from the Run script dialog or from the command line, information about the raw file may be specified before it is opened to prevent the Raw image dialog from opening (select multiple images and right click them in the image listing in the Run script dialog; use the '-r "type;xDim,yDim;xRes,yRes;xUnits,yUnits;endianess;offset"'... option from the command line).
  • Fixed the scripting of the Invert utility.
  • More image attribute changes are now scriptable:
    • Endianess
    • Modality
• Miscellaneous
  • Changed the handling of image matrices within MIPAV. Images may now have multiple matrices, each marked as being of a particular type (e.g., Scanner anatomical (transform to get the dataset coordinates to axial orientation), or Registration (to another dataset). Multiple matrices are now saved in the MIPAV Image XML file.
  • Removed passing of ViewUserInterface from many class constructors and methods. Call ViewUserInterface.getReference() instead. Plug-in methods using ViewUserInterface have been deprecated and will be changed to remove the ViewUserInterface parameter in 3 months.
  • Fixed painting so that it follows the user's cursor as expected when approaching the border of a pixel.
  • The Screen capture utility now adds '_screenCapture' to the name of the original image when naming the generated image and keeps the dialog open after each capture to facilitate capturing multiple windows.
  • Resetting the LUT for RGB images now updates the image immediately.
  • Performing a Quick LUT will now update the Histo/LUT dialog immediately if the dialog is visible.
  • Fixed the Otsu and Maximum entropy thresholds.
  • Added the ability to select the RGB components of the applied paint (and optionally keep the original image date intact for the other channels).
  • Added right click menus to the Quick mask and Paint-to-mask toolbar buttons to allow for either in-place or into-new-image processing.
  • New toolbar icons have been added to indicate buttons which can have their behavior altered by right clicking on them (e.g., the zoom/unzoom buttons and the masking buttons).
  • Added a new help topic titled 'Connecting to SRB BIRN from MIPAV'.

3.1.3 (03/30/2007)

• File handling
  • Added read-only support for Philips PARREC files (.rec/.frec).
• VOIs
  • Fixed the VOI Flip depth operation.
  • The thickness of the lines which make up a VOI can now be adjusted.
  • Fixed VOI contour smoothing.
• Scripting
  • Many image attribute changes are now scriptable:
    • Orientation
    • Origin
    • Resolution
    • Units
    • Talairach
    • Transform
• Miscellaneous
  • Added ability to create and save custom paint brush shapes.
  • Added the option to only include some intensity levels while painting to the Advanced paint dialog.
  • MIPAV is now available for download and use by researchers from any type of organization (non-profit, government, commercial, or an individual).
  • Fixed some bugs in the display of scanner coordinates when dragging through an image with certain orientations.

3.1.2 (03/05/2007)

• File handling
  • Fixed reading of MIPAV image xml files with unknown orientations.
  • Improved the DICOM browser study and series parsing, sorting and image preview.
  • Fixed a problem reading 2D, 3D and 4D TIFF images. Also reduced memory usage of TIFF reader.
• Algorithms
  • Major problems with the Manual 2D registration tool have been resolved.
  • Documentation for 2D histogram, B-spline registration, Face anonymization, and Transform to power of 2 has been added to the MIPAV help system.
• Utilities
  • Fixed the updating of the image origin after the Crop utility is run.
  • The image Flip utility now can also flip VOIs within the image as well.
• VOIs
  • The points that comprise a VOI are now saved in scanner space when written to MIPAV's xml VOI format, instead of voxel or pixel space.
  • The Flip VOI tool now only flips the selected VOI contours.
  • Re-organized the VOI-related items in the MIPAV menu bar and the VOI right-click menu.
  • Added a new xml format used to save VOI Annotations (a text label with optional arrow) (saved with the extension '.lbl').
  • Fixed the adding of points to VOI contours when the 'Draw new contours without holding [SHIFT]' option is enabled.
• Scripting
  • Added scripting documentation to the MIPAV help system.
• Miscellaneous
  • Allow collapsing of masks/paint to a single value in the Multi-paint dialog.
  • Shortcuts have been added to the Multi-paint dialog for faster paint mask editing.
  • Plugins packaged as tar and tar.gz files may now be installed in MIPAV.
  • Plugins may now be assigned keyboard shortcuts using the Shortcut editor.
  • Fixed SRB uploading of xml/raw image datasets.
  • Fixed a bug in downloading and opening .nii files from an SRB repository.

3.1.1 (02/07/2007)

• File handling
  • Fixed a bug where saving an image multiple times to analyze, spm, or nifti format would cause an error.
• Algorithms
  • Fixed a bug that would occur when OAR was run on an image with no VOIs.
  • Updated the help for the FRAP algorithm to better reflect the equation used.
• Image views & visualization
  • Re-enabled the radiological voume view in the Tri-Planar view.
  • The Tri-Planar views can now be zoomed in and out independently using two new buttons. After clicking the one of the independent zoom buttons click within one of the Tri-Planar views to zoom it; hold down the shift button to continue zooming.
• Scripting
  • Re-enabled the ability to delete images and VOIs selected for use in a script from within the Script Run dialog.
  • The Script Toolbar now shows each script's filename, not the whole path.
• Miscellaneous
  • Holding down the shift key while clicking the previous slice/next slice buttons or using the mouse scroll-wheel with an image selected now synchronizes the current slice displayed for all images with the same number of slices as the current active image.
  • Left-clicking within an image now displays the position and intensity of the image location the mouse is placed over next to the mouse cursor. The color of this text can be changed through the MIPAV options dialog.
  • Re-enabled the q -> quickLUT default shortcut that was disabled in version 3.1.0.
  • MIPAV plugins stored as tar and tar.gz files can now be installed into MIPAV.

3.1.0 (01/26/2007)

• File handling
  • Fixed some image position tag precision errors when reading and writing DICOM files.
  • Fixed DICOM communication compatibility problems with the GE and XNAT DICOM servers.
  • Improved handling of saving of files without providing a file extension in the Save image as dialog.
• Algorithms
  • Adaptive median filter added.
  • Added documentation for Maximum likelihood iterative blind deconvolution algorithm.
  • Added support for 2.5D processing in the Fill objects algorithm.
  • Fixed a problem in detection of errors encountered while executing the 2.5D BSpline registration algorithm.
  • Resolved problems which prevented context-sensitive help for some algorithms from appearing correctly.
  • The Threshold algorithm now can produce a masked image (of the same type as the original image), a binary mask, or a short mask.
  • Added 2.5D processing capability to the Level set and Level set diffusion algorithms.
  • Fixed a bug in Histogram generation with the VOI XOR option enabled.
  • Improved face anonymizer algorithm results.
  • Fixed some problems in the 2D Histogram calculation and visualization.
  • Added Cumulative histogram algorithm.
  • The BET Brain extraction algorithm initial center of mass calculation has been improved.
  • Fixed a bug in the Manual 2D serial registration tool on Linux systems.
  • Added Histogram matching documentation.
  • The Optimized automatic registration methods now automatically transform any VOIs in the source image into the space of the result image.
• Utilities
  • Fixed bug in X and Y axis rotations.
  • Fixed bug in progess bar of the Flip utility.
• VOIs and painting
  • Multiple improvements to the multi-paint tool (mask intensity values are now editable, VOI import/export added).
  • VOI interiors can now be shown with a semi-opaque or fully opaque coloring.
  • Added a button to the paint toolbar to toggle display an opaque border around painted regions.
• Image views & visualization
  • Added support for texture mapped or per-vertex intensities from an arbitrary image volume onto surfaces in the Texture-mapped Volume renderer.
  • Added the ability to paint on surfaces with a variety of tools in the Texture-mapped volume renderer.
  • Added Maximum intensity projection view of a 3D volume.
  • Fixed an issue with Talairach visualization in the Tri-planar view.
• Scripting
  • Fixed a minor scripting bug in the Replace value utility.
  • Fixed the saving and loading of the image and VOI file selections from the Script run dialog.
• Miscellaneous
  • Fixed the setting of default keyboard shortcuts in MIPAV.
  • Fixed window resizing and freeze-up problems which occurred on some systems.
  • Image endianess can now be altered in the Image attributes dialog.

3.0.1 (11/22/2006)

• File handling
  • Fixed 'Save image' for XML images (was saving to imagename.xml.raw).
  • MINC modality attributes are now read by MIPAV, if present.
  • The Save DICOM dialog now sets the modality chooser (for DICOM tag 0008,0060) based on the image's modality.
  • When saving a PET image from another format to DICOM, MIPAV now calculates the intensity rescaling slope and intercept for each slice, allowing for floating point intensities to be stored.
  • MIPAV now sets the image valid-range attribute in MINC headers it writes based on the range of the type of data being written instead of the image intensity ranges (e.g., -32767 to 32767 for a short image). Using the intensity ranges caused problems when the image's minimum and maximum values were too close together and the data was being rescaled to from short to floating point values.
  • Corrected a bug in how MIPAV calculated the x start and y start attributes for MINC images. They are now centered within the first voxel of the image.
• Algorithms
  • Thresholding (Algorithms -> Segmentation -> Threshold) can now produce a short mask image.
  • Optimized the memory management of the Maximum likelihood iterated blind deconvolution algorithm (Algorithms -> Microscopy -> Restoration -> Maximum likelihood iterated blind deconvolution).
• Utilities
  • Fixed the scripting of flipping the Z-axis of an image (Utilities -> Flip -> Depth).
• VOIs
  • A bug in the livewire VOI tool has been fixed.
  • Fixed VOI grid overlay display.
• Image views & visualization
  • Fixed the volume renderer (Image -> Views -> Volume renderers) cube orientation.
  • Fixed a bug in the volume renderer's arbitrary clipping plane.
  • Fixed the linked frame update in the Tri-planar view (Image -> Views -> Triplanar).
• Scripting
  • Improved VOI support in scripting system.
  • Fixed a bug which prevented running a script on multiple images opened from disk.
  • Fixed some drag-and-drop annoyances in the Run script dialog (Scripts -> Run script).
  • Plug-ins may now specify new package locations where MIPAV should look for scriptable actions (see ScriptableActionLoader.addScriptActionLocation(String)).
• Miscellaneous
  • Fixed some minor annoyances in the Multi-paint dialog.

3.0.0-2006-11-14 (11/15/2006)

• A completely re-written scripting/macro system:
  • Improved script readability, robustness, and error reporting.
  • A new, simplified, drag-and-drop interface for executing scripts (Scripts -> Run script).
  • The new system is not backwards compatible. Scripts created with versions of MIPAV before 3.0.0 are no longer supported. Please re-record your scripts using MIPAV 3.0.0 or above..
  • Installers for the last nightly build of MIPAV before our integration of the new scripting system are available upon request.
• The MIPAV coordinate translation system has been consolidated, improved, and simplified.
• A MIPAV installer for 64-bit linux systems is now available from our downloads section.
• An upgrade to the version of InstallAnywhere that we use to create MIPAV's installers should result in the resolution of a number of installer problems on 32- and 64-bit Linux systems.
• A new and improved progress bar system for algorithms and utilities.
• File handling
  • The Z-dimension resolution in MIPAV is now the distance between the centers of two adjacent slices. It is no longer the slice thickness.
  • The default names given to images stored in clinical file formats uses the general format [study-number]_[series-number] (e.g. 1394_2) instead of the patient or file name.
  • MIPAV is now able to open some file formats when the files do not have extensions, without prompting the user.
  • Multiple images may be opened simultaneously from the Open file dialog (File -> Open image (A) from disk).
  • Added user-defined file filters (Help -> MIPAV options).
  • Fixed the optional saving of XML headers with Analyze image files.
  • Improved the MIPAV XML 3D surface format.
  • Color RAW files with 2, 3, or 4 colors can now be read.
  • Added support for complex double RAW files.
  • Many improvements and bug fixes have been made in the following formats:
    • Bruker
    • DICOM
    • GE Sigma 5X
    • Magnetom vision
    • MINC
    • NIfTI
    • XML multi-file datasets
  • The following file formats are now supported:
    • GE Sigma 4X
    • MGH / MGZ
    • NRRD
• Algorithms
  • A bug in the Erosion (Algorithms -> Morphological -> Erode) and Dilation (Algorithms -> Morphological -> Dilate) morphology operations has been fixed.
  • Some improvements have been made to the IHN3 correction algorithm (Algorithms -> Shading correction -> Inhomogeneity N3 correction)
  • Algorithms to calculate Signal-to-noise ratios for MRI images has been added (Algorithms -> SNR)
  • The Fuzzy C-Means algorithm (Algorithms -> Segmentation -> Fuzzy C-means -> Single channel) now produces unscaled probabilities in a float image instead of probabilities scaled by the input image intensities when performing a fuzzy segmentation.
  • The Fuzzy C-Means algorithm now labels the classes it produces 1, 2, 3, ... when performing a hard segmentation.
  • Added non-negative garrote and SCAD thresholding to Wavelet thresholding algorithm (Algorithms -> Filters (wavelet) -> Thresholding).
  • Fixed a matrix bug in the Transform algorithm (Algorithms -> Transformation tools -> Transform).
  • The Extract surface algorithm (Algorithms -> Extract surface (marching cubes)) now allows for blurring before surface extraction.
  • Improved memory management in a few algorithms.
• Utilities
  • The Mask utility has been renamed to Fill image (Utilities -> Fill image).
  • The Pad slices utility has been renamed to Pad slices to power of 2 (Utilities -> Slice tools -> Pad slices to power of 2).
  • Improved memory management in a few utilities.
• VOIs
  • An internationalization error in the VOI statistics generator (VOI -> Statistics generator...) has been fixed.
  • Added a continuous contour VOI drawing option (without holding down the Shift key) (Help -> MIPAV options).
• Image views & visualization
  • Added neurological viewing convention to the Volume Renderer's (Image -> Views -> Volume renderers) Tri-Planar view.
• Miscellaneous
  • The PowerPaint tools have been improved.
  • ImageB can now be separated from the ImageA it is loaded with (File -> Extract image (B))
  • The T key may be used to toggle between viewing ImageA and ImageB intensities when two images are loaded.
  • A number of obsolete plugins distributed with MIPAV have been removed.
  • Running a script with the -hide command line option automatically causes MIPAV to exit once the script has completed.

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).

1.60 (01/13/2006)

• 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

1.59 (12/12/2005)

• 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.

1.58 (11/18/2005)

• 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.

1.57 (10/28/2005)

• 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)

1.56 (10/14/2005)

• 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.

1.55 (09/30/2005)

• 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.

1.54 (09/26/2005)

• 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.

1.53 (09/12/2005)

• 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).

1.52 (09/02/2005)

• 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.

1.51 (08/26/2005)

• 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.

1.50 (08/19/2005)

• 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.

1.49 (08/12/2005)

• 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.

1.48 (08/05/2005)

• 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.

1.47 (07/29/2005)

• 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.

1.46 (07/22/2005)

• 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.

1.45 (07/15/2005)

• 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.

1.44 (07/08/2005)

• 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.

1.43 (07/01/2005)

• 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.

1.42 (06/28/2005)

• 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.

1.41 (06/27/2005)

• 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.

1.40 (06/20/2005)

• 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.

1.39 (06/09/2005)

• 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).

1.38 (06/02/2005)

• 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.

1.37 (05/24/2005)

• 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.

1.36 (05/13/2005)

• 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.

1.35 (05/10/2005)

• 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.

1.34 (05/06/2005)

• 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/.

1.33 (04/21/2005)

• 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.

1.32 (04/07/2005)

• 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.

1.31 (03/07/2005)

• 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.

1.30 (02/10/2005)

• 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

1.29 (01/13/2005)

• 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

1.28 (12/21/2004)

• 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.

1.27 (12/02/2004)

• 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

1.26.3 (11/22/2004)

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

1.26 (11/19/2004)

• 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

1.25 (11/03/2004)

• 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

1.24 (10/18/2004)

• 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

1.23 (10/08/2004)

• 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

1.22 (09/28/2004)

• 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

1.21 (09/21/2004)

• 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

1.20 (08/31/2004)

• 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

1.19 (08/30/2004)

• 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.

1.18 (08/25/2004)

• 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

1.17 (08/24/2004)

• 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

1.16 (08/06/2004)

• 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

1.15 (07/23/2004)

• 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

1.14 (06/30/2004)

• 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

1.13 (06/25/2004)

• 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

1.12 (06/10/2004)

• 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

1.11 (05/26/2004)

• 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

1.10 (05/18/2004)

• 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

1.09 (05/05/2004)

• 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.

1.08 (04/13/2004)

• 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

1.06 (03/17/2004)

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

1.05 (03/09/2004)

No changes listed.

1.04 (03/08/2004)

• 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

1.03 (03/02/2004)

• 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.

1.02 (02/11/2004)

No changes listed.

1.01.2 (02/10/2004)

• API organization glitches have been worked out.

1.01.1 (02/10/2004)

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

1.01 (02/09/2004)

• 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

1.00.0 (01/23/2004)

• 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

0.999U (01/09/2004)

No changes listed.

0.999R (12/04/2003)

• Now reads and writes ICS images
• Redirect output to log file
• More file formats are available in the file filter. Check the options after installing this version
• added ability to hold onto more than just the last 4 loaded images
• DICOM reader includes more advanced DICOM sequence processing. DICOM save may be adversly affected.

0.999Q (11/12/2003)

• Shortcut saving a user-defined LUT button added to the LUT dialog
• Updates to RayCast renderer: faster, among other improvements
• Seperable kernel added as option for blurring; option is much faster, but consumes a great deal more memory
• Improved shear warp renderer
• DICOM reader has some fixes for problems introduced because of 4D support
• Additional license information added to the about-file
• Previous bundled linux JRE had some problems; it has been changed, but is still being tested

0.999P (11/12/2003)

• Shortcut saving a user-defined LUT button added to the LUT dialog
• Updates to RayCast renderer: faster, among other improvements
• Seperable kernel added as option for blurring; option is much faster, but consumes a great deal more memory
• Improved shear warp renderer
• DICOM reader has some fixes for problems introduced because of 4D support
• Additional license information added to the about-file

0.999N (10/29/2003)

• XML schema includes thumbnails
• Improve ray cast volume renderer and image capture for movie imaging
• Improved Surface Renderer
  • Image capture for Movie
  • Opacity function options and R/W
  • Clipping plane for eye
• Improved Macro robustness
• DICOM reader can now handle GE FastCard 4D datasets
• Improved Image Browser
  • Display of thumbnails
  • Faster and uses less memory
• 3.5D OAR registration
• More documentation in the Help files
• Improvments to the secure file transfer and chat GUI
• Secure file transfer and chat uses a new version of the SSL implementation

0.999M (10/1/2003)

• The bundled JVM is now Java 1.4.2.01, with Web Services 1.2.1 for XML support and Java 3D 1.3.1.
• To improve program responce, we are now pre-processing source code using Dash-O as an optimization tool.
• Coherence diffusion and regularised isotropic diffusion support:
  • 2D
  • 2.5D
  • 3D
  • both color and greyscale
• Crop uses less memory
• Scripts can now save data from the Data Window
• Maximum Intensity Project and Digital Reconstruction Radiograph modes have been added to the interactive volume renderer.
• Improved Surface Renderer
• Added surface smoothing method that does not shrink, leaving total volume approximatly the same.
• OAR registration is more robust
• Added a "Global Data" area to the output Data Window
• Added ability to read LZW Compressed TIFF and LSM file formats
• Added Brightness and Contrast controls to DICOM and Image browsers.
• Refined Co-localisation for Microscopy

0.999a (8/20/2003)

• We again support the MAC OS X platform!
• Major improvements to the surface visualization tool.
  • Added 3D and 2D texture VOLUME visualization with opacity control.
  • Improved coordination with tri-planar view. For example, selecting a position on a surface in the surface viewer automatically updates the tri-planar view to the same location.
  • Opacity of surfaces, volume and cut planes can be selected by the user.
  • Improved visualization recording for making movies.
  • Stationary light has been added.
  • New toolbar for quick access to tools
  • Many more improvements.
• Added ability to read and write SPM formatted files (similar to Analyze format).
• Added ability to write simple AFNI formatted files. We already read AFNI formatted files.
• Improved image cropping utility. Origin information correctly updated.
• Improved add image margin utility. Origin information correctly updated.
• Changes to the Surface extraction algorithm (see algorithms -> extract surface):
  • retains image coordinate space information
  • triangle consistency check is implemented to insure all triangle are all either CW or CCW.
• Improved the DICOM receiver to catch images from the Kodak AutoRads. The Clinical Center had recently upgraded to a new version of software on the AutoRads.
• Improved general functionality to the image transform algorithm GUI.
• The bounding box of a VOI now displays the origin, width and height in both pixels and units of measure (eg. mm) and position information.
• From the animate player added ability to save color AVIs so that VOI contours would retained. Option to still save in greyscale with RLE is available. Grey scale RLE encoded AVI are much smaller but you lose VOI information. Also ability to save in other compression formats including: MPEG4 version 2, MPEG, and Quicktime. New compression formats require a separate installation of Java Media Framework.
• Autocorrelation and autocovariance calculation algorithms added.
• Colocalization algorithm added. This algorithm is based on Costes and Locketts' method.
• Improved scripting tool.
• Reduced memory usage in Utility -> Convert Type. This utility is used to convert from one image type (byte) to another image type (float) and its data range.
• Improved Utility remove slices. User can now specify a range.
• OAR 2.5D (2D time series) registration now uses much less memory.
• Save specified DICOM tags into our XML file format.
• Improved Livewire segmentation, faster, more robust and ability to remove last achor point with a right mouse click
• Subsample by 2, 4, or 8 utility now available.
• New algorithm to tranform image so that each image dimension is a power of 2. Used with volume visualization tool

0.997t (3/21/2003)

• Secure file transfer functionality added to the file menu. Use SSL java library to setup a secure link using RSA128 encryption. File transfer includes automatically zipping the file(s), securely sending the zipped file, unzipping the file and saving the received files on the receiver's local drive.
• New non-linear smoothing method that smoothes along an optimal path.
• Upgraded and validated DICOM query and retrieve functionality on Kodak and AGFA PACS achieves.
• Found and fixed memory leak in utility to remove image slices.
• Improve macro recording.
• More algorithm documentation
• Added memory check. MIPAV resets memory allocation to 100M during reinstallation. Upon starting MIPAV for the first time after reinstalling, memory is settings are checked and the user is notified if the old memory allocation is different from the 100M. The user then can select the old memory settings.
• AVI writing improvements. RLE option decreases file size.
• Many other small improvements and bug fixes.

0.997d (2/14/2003)

• Fixed memory leak in the utility to convert a _3D_ image to 4D image set.
• Added a new algorithm to evolve a triangulated surface using the GVF.
• Fixed a bug that could hinder saving 4D datasets in the MIPAV XML format.
• Slider value fixed for 4D images and the lightbox view.
• Faster DICOM file reader, for some images speed increase by as much as ~200%.
• Two new adaptive filters smoothing filters. Algorithms -> filters (spacial) -> Adaptive noise reduction and Adaptive smooth. See MIPAV help for explanation of the algorithms. For 2D images.

0.997a (2/4/2003)

• Enhancements
  • New web page!
  • Online help using JavaHelp for many algorithms -- more to come. For example see Algorithm -- Filter (spacial) - Gaussian Blur.
  • Link two images together so that they scroll together. Works also in the Tri-planar view.
  • New MIPAV file format based on XML. The XML Schema for the file format is in the file image.xsd. This file is located in the mipav install directory.
    • The XML formatted header file is stored in a separate file and stores a link to the image file.
    • The XML file is a text format easily viewed with any text editor as well as internet browsers.
    • The MIPAV Schema is flexible and allows for many optional tags. For example. The users may (optional) add [0 -- infinity] parameters that have the form Name, Description, Value type, Value, and Date/time.
    • Saves LUT, matrix, resolution, axis orientation information.
    • Link to another image so that the linked image is automatically opened. See menu: Image->Attributes->edit attributes
  • Crop and Add image margins utilities now correctly retain and/or update important image tag information like image origin, image orientation, dimensionality, etc.
  • Modified internal parameters of the brain extraction algorithm to be more robust and improve segmentation (less tissue included anterior -- near the eye).
  • Levelset segmentation added
  • When the cursor is in an image, right click and hold the button and move the mouse to adjust window and level of the image. Level is changed by moving the mouse up(+) and down(-). Window is changed by moving the mouse right (+) and left(-).
  • A utility function to convert a series of images loaded as a _3D_ dataset into 4D dataset.
  • Added utility to save a 4D image to a series of 3D volumes and save a 3D image to a series of 2D images.
  • Undo last VOI change.
  • VOIs are now saved in one of two formats *.voi and *.xml. See voi.xsd schema that describes the new VOI format.
  • Watershed segmentation algorithm automatically saves the gradient magnitude image to a file. The next time the Watershed algorithm is called, it will automatically load gradient mag. image that that it doesn't need to be recalculated.
  • Image and DICOM browser are faster and have a better GUI.
  • Option to smooth a contour using a Bspline. See menu VOI -> smooth VOI.
  • Two options added to OAR3D registration:
    • Subsample image can be turned off -- only select for small images.
    • Option to skip search -- jumps directly to last optimization. Only choose this option if the images are approximately aligned (~5 degrees, 10 mm). This makes the registration twice has fast but accuracy or ability to converge could be reduced.
  • OAR 2.5D and 3.5D registrations algorithms where rigid registration was requested, a graph of the resultant translations and rotations is produced.
  • OAR 3.5D added an option to select a reference volume or register to an average volume
  • Improved the speed of 2D, 2.5D and 3D OAR registration by 25% - 30%.
  • A button has been added to the top toolbar to propagate a contour of a VOI to all slices.
  • A middle mouse click in the 2D image frame will cause the triplanar view to update to that location (if open).
  • Remove GUI bugs for VOI boundary evolution algorithms.
  • Option to ask user before closing frame -- see Help->Mipav Options.
  • Image frame registry displays image frames and images and allows the user to bring a selected frame to the front.
  • Updated DICOM anonymization to include the option toanonymize UIDs.
  • Upgraded to newer DICOM3 element dictionary.
  • Manual (semi-manual) registration tool now allows the user to select two 2D images to register or a 2.5D (2D images where the 3^rd dimension is time) time series. Many GUI improvements also.
  • Trim parameter (Set from VOI menu ) now works as expected.
• Bugs fixed
  • Read LUTs from a read-only file (e.g. CD).
  • Fixed a bug in Histogram Equalization algorithms
  • VOI retrace mode no longer randomly adds a new point at the origin
  • VOI - bring to front, bring forward, send to back sent backward now work correctly.
  • Bug fix to thin-plate-spline registration method.
  • Found and fixed a number of memory leaks.

0.99x (9/19/2002)

• Added VOI statistics calculator (VOI -> Statistics Generator menu). This dialog allows the users to select all or some VOIs and which statistics to calculate on the selected VOIs. The output is to a file and the log window in tab delimited format. The user is able to indicate weather the statistics can be calculated on a VOI basis or for each contour of a VOI
• File menu now records last four images open for quickly opening often used images.
• DICOM image browser for browsing (thumbnail view), sorting, and opening DICOM images.
• Simple background subtraction algorithm. User identifies background with a VOI and the average or median value is subtracted from the image.
• 4D (3.5D) time series registration based on MCFLIRT (FSL group in UK) called TSOAR.
• Improvements to simplify plugins
• Surface viewer:
  • Added ability to adjust opacity of the surfaces.
  • Fixed a smoothing surface bug.
• Added Adaptive Skeleton Climbing algorithm used to generate surfaces to the algorithms menu.
• Numerous smaller improvements and bug fixes.

Version 0.99u 7/21/2002

• Added 2D and 3D registration for color images (least squares cost function)
• Improvements to image browser (e.g. open full image from thumbnail image)
• Analyze color images can now be read and written
• Fixes to DICOM anonymization tool
• Improved DICOM reader robustness
• Fixed bug is threshold dialog

Version 0.99t (6/15/2002)

• File format improvements and additions
• Read Bruker format
• Read Biorad format
• Read Ziess 510 format
• Read Freesurfer image and surface formats
• DICOM reader can now read lossless JPEG
• Load and save array of images in separate files of type JPEG, PICT, TIFF
• Improved DICOM directory anonymization
• Microcat images can be opened by either selected the .log file or one of the image files .ct
• VOI:
  • Save and Open all for VOIs
  • Select VOI on mouse release -- fixes problem of accidentally moving VOI when selecting it.
  • VOI polygon either open or closed based on selection of last mouse click (last point or first point of the VOI).
  • Euclidian length of VOI ployline is now displayed
• View:
  • Simple window and level tool so that the complete Histogram LUT tool does not need to be opened.
  • Tri-planar view updates image views and position information when selecting a point on a surface in the Surface Render viewer.
  • Lightbox view has many new options for extracting slices and dynamically updating the display of the images.
  • New Image browser. User chooses a directory and a directory tree is generated. The user is then able to scan the directories and quickly view images with relevant image information displayed (dimensionality, voxel size, etc. ).
  • Improved contrast mapping, especially with CT images.
• Algorithms:
  • Added MRI "deskulling" algorithm (based on the Brain Extraction Tool "BET")
  • Advanced image calculator: combine images of sophisticated functions using calculator GUI.
  • Added Histogram matching of two images using their probability density function.
  • Improved adaptive histogram equalization - faster
  • Convert RGB to gray with weightings input by the user option.
  • FFT 2.5D option added
  • Improvements to OAR (Flirt variant) registration
    • VOI option to identify sub regions to be registration.
    • Fix weightings options
    • Improved accuracy and speed
  • Upgraded to AIR 5.07
  • Livewire added (interactive VOI generation). User can select one of three functions to optimize using Dykstra's method. (2D)
    • Gradient information,
    • Laplacian medialness.
    • Intensity.
  • Fuzzy connectedness region grow method is now 2x faster.
  • Principle components filter for reducing noise.
• Many more improvements and bug fixes.

0.99p (3/24/2002)

• Lightbox improvements.
  • Faster and uses less memeory
  • Select and delete image slices
• File format improvements
  • Improved DICOM sequence reader
  • Read MicroCat CT images (select *.log file)
  • Improved MINC writer (faster and uses less memory)
  • Improved MINC reader (more robust)
  • Improved Siemens reader (more robust)
  • Improved MRC file reader
• Surface renderer
  • Improved lighting controls
  • Capture to AVI movie
  • Surface volume calculation
  • View bounding box option
  • Adjust background color
  • Smoothing surface option
  • Save surface to VRML format
  • Added toolar button to invoke surface renderer
• Added Fuzzy Connectedness region grow algorithm
• Simple wavelet denoising algorithm
• Polyline VOI now displays the length.
• Paint to VOI option now available in VOI menu
• Improved screen capture tool (under file menu)

0.99n (1/24/2002)

• 2D and 3D image registration (intensity based) using a choice of least squares, normalized mutual information, mutual information or cross correlation cost function.
• Tri-planar upgrades
  • Radiologically correct orientation of DICOM / AFNI / GE / MINC / SIEMENS formatted images
  • Improved speed.
• Read GE formatted images
• Read and write Interfile format (A nuclear medicine format)
• Improved MINC image format including MINC label files.
• Local normalization algorithm using to reduce intensity gradient across images
• GVF snakes
• Improved surface renderering with the ability to capture to AVI movie format.
• DICOM anonymous tool - anonymize whole directories of DICOM formatted images
• Macro toolbar
• Improved logging
• Transform option include skews
• Improved adaptive histogram equalization
• More interpolation options: 3rd, 5th, or 7th order Lagrangian
• Many user-interface improvements.

0.99c (10/3/2001)

• Major tri-planar upgrades:
  • Correct orientation of DICOM formatted images
  • Ability to put images into Talairach orientation (AFNI-like)
  • Overlay Talairach grid
  • Display DICOM or Talairach cursor position
• Read AFNI images
• Read Siemens' Magnetom Vision format (view all header information).
• Read Metamorph formatted tiff-extended images
• Read/write MINC region of interest files
• Read/write FITS images
• Read/write/modify transformation matrices (MIPAV or FSL format)
• Surface extraction and decimation (triangulated mesh) from VOI.
• Surface rendering tool (triangulated meshes) and orthogonal image viewer.
  • Ability to add multiple surfaces and adjust properties of surfaces
  • Control lighting
  • Zoom/rotate/translate surfaces and record mouse function for playback.
• 3D height surface of 2D images.
• Mathematical Morphology improvements. Now supports edge extraction and skeletonization.
• Graphing component now supports interactive time-activity-curves from point or contour VOIs.
• Image transformation now supports the transformation of VOIs.
• Improved Analyze header viewer.
• Ability to load two images into a single frame with alpha blending without first saving image to a file.
• Newer version of documentation.

V0.99 (6/8/2001)

• MIPAV bundled with Java 1.3.1
• MRI Inhomogenity correction - N3 algorithm is now available (Sled et.al.)
• Adaptive histogram equalization has been added. Significantly improves image contrast
• Checker board for two image display
• Movable window which display a second image over another image. Great tool for checking registration results.
• Read Cheshire formatted images and ROIs
• Automatically determines big or little endian ordering when reading Analyze images
• Image -> attributes -> show header menu item now displays image endianess
• Change endianess using check box found in Utilities convert type dialog
• Enhanced TIFF reader to read "tiled" images
• Improvements to the 2D semi-manual registration tool
• 2D/3D Thin-plate spline landmark registration algorithm added
• Save DICOM tags to a text file.
• 3D orthogonal image viewer using Java 3D
• windowed sinc interpolation option available in algorithm transform
• Improved memory monitor display
• Utility to extract 3D datasets from 4D datasets in any dimension (i.e. extract an image slice from the same location over time).
• Non-maximum edge suppression (i.e. Canny edge) algorithm added

V0.98r (3/16/2001)

• Fixed the annoying menu problem for Windows OS
• Added the ability to save the Lightbox configuration parameters
• User preferences are now saved in the user's directory. Now users no longer need to share a preference file
• Added Dzung Pham's Fuzzy C-Means algorithm for gray, white, and CSF segmentation
• Added additional functionality to the AVI reader
• Read/write Quick time files
• More speed-ups for transform algorithm
• New toolbar buttons for quick access to tri-planar and lightbox views.
• Improved Analyze file format reader
• Users are now able to open a series of 3D images (individual 3D Analyze formatted, consecutively ordered images) into to a 4D dataset in Analyze format. (use File -> open -> multi-file)

V0.98p (1/17/2001)

• DICOM
  • Query/Retrieve improvements (faster & less memory)
  • Now reads multiframe and RGB images
• AVI reader/writer (uncompressed, RLE8)
• Added 4D gradient magnitude and dual-threshold filters
• Added Gaussian blur, gradient magnitude, and median filters for RGB images. Each color channel (r, g, and/or b) can be processed independently and is selected by the user in the respective algorithm dialog.
• "Painting" of complex images and RGB images is now supported. Painting complex images (Freq. domain) allows the user to remove specific artifacts.
• Improved dialog for region grow (paint can) in the paint toolbar
• Bug fix for Morphology operations for odd shaped images
• Significant speed improvements to image transformation algorithm.
• Added algorithm that quantifies image data based on a mask image. This method is available in the Algorithms -> quantification using mask menu. An automated version is in LUT dialog via the Threshold button.

V0.98m (12/8/2000)

• Tri-planar view:
  • Added 3D crop feature
• All views (Lightbox, Tri-planar, 2D planar ) support 3D image with a 4D overlay image. For example: 3D structural MRI and a 4D functional MRI
• Added 4D Gaussian Blur option
• Rotate and Insert image utilities now update DICOM image tags more accurately
• Added Utility function to swap the 3rd and 4th dimensions
• DICOM reader/writer improvements:
  • Anonymize function purges more tags per Supplement 55 of the DICOM spec.
  • Better use of tag information when displaying the image
• Added "Memory allocation" function to adjust the amount of memory that MIPAV uses. Default is 100MB. Be sure to restart MIPAV after changing these values. (The mipav.lax will no longer need to be manually changed)
• Image header information has been moved from Help -> About Image to Image -> Attributes -> View header
• General improvments to the interaction of image views. For example, double clicking in the light box view on a specific image will automatically update the 2D and tri-planar view to that image.
• DICOM images can now be registered based on Image position and orientation tags.

V0.98j

• Tri-planar view will now:
  • allow point VOI adjustment in any of the three views - used for Landmark registration
  • improved display speed
• DICOM reader improvements:
  • now able to read DICOM (via secondary capture images exported from the Cheshire program.
  • improvements to better handle compliant and somewhat non-compliant DICOM images
  • Improved flexibility when exporting non-DICOM images to DICOM images via secondary capture.
• Point VOI improvements:
  • when reading and writing to a file
  • group points in a single VOI
  • improved labeling

V0.98i

• Tri-planar view will now display crosshairs in all three views
• 4 new preset LUTs: red, green, blue, and gray ramp with blue in first location and red in the last location
• Utility to add image margins to an image 2D and 3D
• Animate viewer:
  • will now process and display 4D images
  • allow interpolation when constructing image of a different size for display
• More/updated documention
• Fixed bug that would not allow RGB images to be converted to grayscale
• Improvements to image resample function:
  • aspect ratio lock/unlock
  • size slider

V0.98g

• Tri-planar view will now
  • display 4D images
  • overlays two images with alpha blending
  • improved image alignment
  • painting in all three views
• DICOM Q/R improvements
  • if study and/or series number is missing study and series descriptions now used
  • general improvements to GUI functions
• Improvements to the protractor VOI
• More/updated documention
• Minor bug fixes

V0.98f

• MIPAV is now bundled with JDK 1.3 for Win32, UNIX, Linux but not MAC. MIPAV should now run much faster on the SUN and Linux platforms
• Added protractor to VOI tool bar for measuring angles
• Added a new VOI - landmark registration algorithm which is presently used to register 2D images over time.
• Tri-planar view now has the capability to align images. This is one step to aligning volumes in Talairach space. More functionality to come.

V0.98e

• Fixed bug that affected the display of images on the SUN platform

V0.98d

• Improved DICOM Q/R table to improve layout.
• DICOM file reader more robust when reading images with inaccurate "pixel-padding value".
• Working on tri-planar view
• Working on Fuzzy C-means segmentation
• Added more documentation - see User's Guide web page
• Other minor bug fixes

V0.98c

• Fixed bug introduced in V0.98b that caused DICOM Q/R and send problems
• VOI size can now be interactively modified using the VOI's bounding box
• Lightbox view now using less memory
• Added more functionality to Tri-planar view - still adding more

V0.98b

• Fixed bug that caused MIPAV not to execute if the mipav.preference file was missing
• Quick LUT - new toolbar button to draw a box in the image. The min and max of the area bounded by the box are used to remap the LUT. Saves time so one does not need to open the full LUT dialog.
• Manual registration now reads/writes landmark points from a file and uses them as imput to a least squares algorithms for 2D registration.
• Read DICOM images in order by: Position if x,y,z dimensions are all spacial. If position is the same for each image slice (i.e. x,y, time) then Order by Instance Number. If the Instance Number is not in the header then Order by the file order in the directory
• Improved MINC file writer
• Interactive levelset VOI now works with RGB images
• Uses less memory in Cine loop.
• Paint feature more robust on various platforms

Version V0.98

• Improved DICOM file reader/writer.
• Improved netCDF/MINC file reader/writer.
• Any file type (i.e. DICOM, raw) to MINC dialog.
• Added install/remove plugins methods.
• Added orthogonal (tri-planar) viewer - more functionality to be added.
• Fixed bug that would not allow RGB images to be displayed in Lightbox viewer.
• Added function under Utilities menu to rotate 3D volume 90 degrees in the 3 orthogonal directions (x,y,z).
• Fixed FFT bug.
• Improved Watershed algorithm to use a little less memory.
• Added (2D) manual registration tool under Algorithms -> Registration.
• Added method to control the automatic trimming of VOI points (see VOI menu).
• Improved DICOM sanitization (more tag options).
• Added ability to disable DICOM receiver (see Help menu).

Version V0.97a

• Debugged and tested query and retrieve on Kodak/Cemax PACS
• Tested and verified MIPAV as a receiver of images from the Kodak/Cemax Autorad device.
• Improved Query and retrieve from GE PET scanner.
• Improved DICOM PET file reader.
• MIPAV to MIPAV DICOM send/receive function.
• DICOM - Verification function added. Used to test host connectivity.
• Fixed bugs in Graph module.
• Added animation viewer for showing movies.
• NetCDF and MINC file reader / writer.
• Flip images ( x or y axis).
• Fixed bugs in image transformation.
• Fixed bug when generating VOI using interactive level set.
• Mask to VOI function added. (Converts mask image (binary - short) to VOIs).
• Added function to convert 3D gray-value dataset to 3D RGB dataset.
• Paint region grow now uses (First In First Out) FIFO data structure. Also added parameters to limit size and/or distance from the seed point.
• Paint toolbar paint intensity level now displays the correct value.
• Paint can (i.e. region grow) now has one level of undo.
• Add Bspline snake algorithm (2D and 2.5D).
• Fixed 3D RGB (TIFF) write bug.
• Misc. bug fixes and speed improvements.