Version 2.65 - 2.651 (25.04.2020)
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • The deployed version of MIB comes with R2019b instead of R2017a
  • Added Drag and drop files into the Image View panel
  • Added dialog with 30 new image filters (Menu->Image->Image filters...)
  • Added dataset alignment using AMST: Align to Median Smoothed Template (Menu->Dataset->Alignment)
  • Added wound healing assay (Menu->Tools->Wound healing assay)
  • Added transformation of Z to C (Menu->Dataset->Transform...)
  • Added additional options to the batch processing: file loop/combine files -> current MIB directory; selection/removal of multiple directories in the Directrory loops
  • Added backup of the full mibImage class
  • Added full backup for dataset transform, resize, crop operations
  • Added squeezing of material indices for models with more than 255 materials (Segmentation panel->Squeeze button)
  • Added a new key shortcut ('n') to increase index of the active material by 1 for the models with more than 255 materials
  • Added saving snapshots in PNG format
  • Added measurements to restore shuffled datasets
  • Updated resampling for batch processing mode
  • Swapped Log and Info buttons in the Path panel
  • Tweaked names of plugins to include spaces between capital letters
  • Optimized handling of Java classes
  • Updated Bio-Formats to 6.4.0 (requires Matlab R2017b or newer)
  • Plugins: Surface Area 3D - a plugin for analysis of 3D surfaces and contacts (Menu->Plugins->Organelle analysis->Surface area3D)
  • Plugins: Spacial Control Points to generate a set of random points over the masked area (Menu->Plugins->Plasmodesmata->Spatial control points)
  • Plugins: Cell Wall Thickness to calculate thickness of cell walls (Menu->Plugins->Plasmodesmata->Cell wall thickness)
  • [2.651] Added smoothing of multiple materials of models via batch processing
  • [2.651] Fixed definition of the starting point for the Membrane ClickTracker tool
  • [2.651] Fixed setData method for specific materials of the model

    Version 2.60 (10.10.2019)
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • The deployed version of MIB comes with R2019b instead of R2017a
  • Added the Batch mode for repetitive processing of images (Menu->File->Batch processing)
  • Added visualization of models using Matlab Volume Viewer app (Menu->Models->Render model->Matlab volume viewer, R2019 or newer, Matlab version only)
  • Added Drag & Drop materials to the segmentation tools (Segmentation panel->Drag and Drop materials)
  • Added content-aware fill using coherence transport (Menu->Image->Tools for images->Content-aware fill, R2019a and newer)
  • Added debris removal tool to automatically or menually remove debris from volumetric datasets (Menu->Image->Tools for images->Debris removal)
  • Added alignment of color channels using landmark multi points (Menu->Dataset->Alignment->Algorithm:Color channels, multi points)
  • Added use of Oriented FAST and rotated BRIEF (ORB) points for automatic alignment (Menu->Dataset->Alignment, R2019 or newer)
  • Added optional correction for instant jumps during running average correction of the drift alignment algorithm
  • Added possibility to add material name and object id during export of quantitation results from the Statistics Dialog to the annotation layer
  • Added export of results from the Statistics Dialog to comma-separated values
  • Added copy to the system clipboard the columns from the the Statistics Dialog (right mouse click over the table and select Copy column(s) to clipboard)
  • Added batch modification of values and coordinates for the annotations
  • Added 4D options to "Material to Selection" and "Material to Mask" options for the context menu of the Segmentation table
  • Added calculation of quantile for automatic contrast stretching (View settings->Display->Right click over the min/max buttons)
  • Added ("Ctrl+E) key shortcut to toggle between current and previous image container
  • Added export of graphs from the graphcut workflow to 3D Lines for visualization
  • Rewritten Image arithmetics to include mask, model, and selection layers (Menu->Image->Tools for images->Image arithmetic...)
  • Updated use of xlswrite, for R2019a or newer writecell function will be used
  • Updated data conversion from 32-bit to 8- and 16-bit; from 8-bit to 16-bit
  • Updated Bio-Formats to 6.2.1 (Requires Matlab R2017b or newer)
  • [2.601] Bug fixes
  • [2.601] Added export of annotations to CSV format

    Version 2.51-2.511 (13.03.2019)
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • Added methods for automatic global black-and-white thresholding (Menu->Tools->Semi-automatic segmentation->Global thresholding)
  • Added selection of materials for rendering of Matlab Isosurface models (Menu->Models->Render model->Matlab isosurface)
  • Added calculation of images with extended depth-of-field focus stacking (Menu->Image->Tools for images->Intensity projection->Focus stacking)
  • Added export of the supervoxels from Graphcut to a model
  • Added saving of HDF5 format in the virtual mode without loading of complete stack
  • Added saving of AmiraMesh files as a sequence 2D sections (Menu->File->Save image as->Amira Mesh binary file sequence)
  • Added an option to display an orthoslice during visualization of 3D lines
  • Added tip of the day window (Menu->Help->Tip of the day)
  • Added H-maxima and H-minima transforms to Mask generators (Mask generators panel->Morphological filters)
  • Added Single Mask object per dataset option when cropping objects from the Get Statistics dialog
  • Improved performance when several materials are removed from the model
  • Improved the Image arithmetics dialog (Menu->Image->Tools for images->Image arithmetic...)
  • Updated BioFormats reader to use Memoizer class, this should hopefully fix Java memory leaks, temporary directory can be specified in Menu->File->Preferences->External dirs
  • Updated sorting of the Get Statistics dialog
  • Fixed initialization of 3D hardware rendering of models
  • Fixed pixel size when combining 2D images with different dimensions
  • Fixed adding icons to buttons when MIB is installed in network path that starts from "//"

    Version 2.50-2.501 (21.12.2018)
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • Added hardware accelerated 3D volume rendering (Menu->File->Render volume->MIB rendering). The volume rendering can be used also for making snapshots and animations. Requires Matlab R2018b or newer!
  • Added automatic image alignment using detected features
  • Added 20 distinct colors palette
  • Added center point marker for the image axes (Toolbar->center point button)
  • Added shuffling of annotations to the randomizer tool (Menu->File->Rename and shuffle)
  • Added delete multiple materials from the model at once (the '-' button in the Segmentation panel)
  • Added split color channel mode for videos (Menu->File->Make movie)
  • Added possibility to change default filters for images (Directory contents panel->Filter combobox->Right mouse click)
  • Added contrast normalization for all layers
  • Added fuse of annotations during fusing of cropped models (Menu->File->Chopped images->Import->Fuse)
  • Added auto removal of spaces in material names when exporting models to Amira
  • Added loading of masks that are smaller or larger than the depth of the dataset
  • Added alternative way to specify a frame around the dataset (Menu->Dataset->Transform->Add frame)
  • [2.501] Added swap slices option (Menu->Dataset->Slice->Swap slices)
  • Improved Lasso mode in the segmentation tools
  • Updated Bio-Formats to version 5.9.2
  • Fixed some compatibility issues with R2018b
  • Fixed a bug in the object separator tool
  • Fixed instructions how to calibrate dataset using the scale bar tool
  • Fixed update of the current color channel after conversion to grayscale
  • Fixed conversion from multicolors to grayscale
  • Fixed insert of a new datasets into the open dataset
  • Fixed a bug of non working scroll wheel after aligning two datasets
  • Fixed combine files as color channels mode
  • Fixed missing values for annotations when imported from matlab workspace together with the model
  • Fixed computation of statistics for the models with 255 materials
  • Fixed of cropping of the selection layer for models with more than 63 materials
  • Fixed alignment for models with more than 63 materials
  • [2.501] Fixed rendering of combined image in the split color channel mode with Lut enabled in Snapshot and Make movie tools
  • [2.501] Fixed Copy Slice for the Insert mode

    Version 2.40 (31.08.2018)
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • Added virtual mode for datasets that are compatible with the BioFormats library or in HDF5 format
  • Added shift of annotations when inserting a slice
  • Added shift of annotations when deleting a slice or a frame
  • Added Segment All function to the graphcut image segmentation in the grid mode to enable segmentation of all subvolumes
  • Improved performance when showing multiple 3D lines
  • Updated BioFormats to 5.9.1
  • Bug fixes

    Version 2.30 - 2.301 18.05.2018 (21.06.2018)
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • Added Lines3D class for 3D measurements and generation of 3D skeletons and graphs (Segmentation panel->3D lines)
  • Added the Image arithmetics dialog (Menu->Image->Tools for images->Image arithmetics...)
  • Added Rename and Shuffle tool (Menu->File->Rename and shuffle) to shuffle images for blind modeling and restore the models back to the original sets of images
  • Added alignment using multi-point landmarks (Menu->Dataset->Alignment)
  • Added export of volumes and models for rendering to Matlab VolumeViewer application (Menu->File->Render volume->Matlab volume viewer or Menu->Models->Render model->Matlab volume viewer, only the Matlab version of MIB, requires Matlab R2017a and newer)
  • Added calculation of 3D skeleton and morphological operations for 3D objects: Menu->Selection->Morphological 2D/3D operations, (only for Matlab R2018a and newer)
  • Added options to insert an empty slice into the dataset (Menu->Dataset->Slice->Insert an empty slice) and to insert an existing slice into another position (Menu->Dataset->Slice->Copy slice...)
  • Added modification of Imaris path from MIB preferences: Menu->File->Preferences->External dirs, please remove IMARISPATH variable from the system environmental variables
  • Added quantitation of objects in physical units (Menu->Models->Model statistics...)
  • Added recentering the view after click for the Membrane ClickTracker tool
  • Fix of cropping objects to files from the Get Statistics tool
  • [2.301] Added filter for filenames to the Shuffle and rename tool

    Version 2.22 16.03.2018
  • Added value field for the annotations, thus each annotation can be weighted based on its value
  • Added possibility to do deep neural network denoising on GPUs with small memory, use the GPU block parameter in Image filters->DNN Denoise
  • Added the Simplify button to the Dataset Info window to allow remove most of metadata
  • Added rendering with Imaris models generated in Matlab (Menu->Models->Render model->Matlab isosurface and export to Imaris), require Imaris 8
  • Added rendering of annotations as scaled spots in Imaris
  • Added rendering snapshots with white background (Toolbar->Snapshot tool->white Bg)
  • Added Get Statistics for models with more than 255 materials
  • Added calculation of Min/Max/Mean/Median intensity projection Menu->Image->Tools for images->Intensity projection...
  • Added use of external BMxD filters [Matlab version only!] (Image filters panel->External: BMxD)
  • Added Add Frame tool that can be used to generate a frame around dataset with a distinct color or using various repetition methods (Menu->Dataset->Transform->Add frame)
  • Added renaming of annotations (Menu->Models->Annotations->Annotation list->RMB over the list of selected annotations->Rename selected annotations...)
  • Improved movie rendering performance for the ROI mode
  • Updated the Image Filter panel
  • Fix of error when opening Images->MorphOps->Morph Closing
  • Fix callback when selecting color channels in the Selection panel
  • Fix of opening of Amira Mesh files with extended headers

    Version 2.21-2.211 21.12.2017
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • Added model with 4294967295 materials for tests
  • Improved object picker for models with 65535 materials
  • Updated TripleAreaIntensity plugin (ver. 2.211)
  • Fix compiling of certain function using the |-compatibleArrayDims| switch to be compatible with the new Matlab API
  • Fix of 'Fix selection to material' switch for models with more than 255 materials
  • Fix connection to Omero for the deployed version
  • Fix, the contains function replaced with ismember for compatibility with Matlab 2014b-2016a (ver. 2.211)
  • Fix of lost key press callbacks after modification of the segmentation table (ver. 2.211)
  • Fix of loading hdf5 datasets with time dimension (ver. 2.211)
  • Few other minor bug fixes (ver. 2.211)

    Version 2.20 14.11.2017
  • Added a new 3D Grid mode to the Graphcut tool; when used the fast interactive performance can be achieved even with very large datasets Menu->Tools->Semi-automatic segmentation->Graphcut
  • Added denoise of image using deep neural network (Image Filters Panel->Filter->DNN Denoise), requires Matlab R2017b or newer and Neural Network Toolbox
  • Added export annotations to Imaris (Menu->Models->Annotations->Export to Imaris as Spots)
  • Added insert of a dataset as a new time point: (RMB over the file name -> Insert into the open dataset)
  • Added possibility to do not calculate intensity profiles for measurements to make measurements faster
  • Added buttons to magnify snapshots in x2, x4, and x8 times using the Snapshot tool
  • Added reading of material names and colors when opening AmiraMesh models
  • Added utilization of the block mode for calculation of object properties for the 3D objects in the XY orientation
  • Rearranged the Graphcut, Watershed and Object separation tools to separate functions under Menu->Tools
  • Updated the Crop tool, the interactive mode allows to modify the selection of the area for cropping before accepting it
  • Updated calculation of curve lengths in the Get Statistics dialog, now the points are smoothed with average filter of 3
  • Updated connection to Imaris
  • Updated BioFormats to 5.7.1
  • Updated inputdlg to customizable mibInputMultiDlg function
  • Updated measure line/freehand length tool (Menu->Tools->Measure), now after use of these tools the selection is not shown
  • Fixed disabling of the selection mode after modification of measurements
  • Fixed movement of measurements after their recalculation
  • Fixed recalculation of voxels after import of images from Matlab
  • Fixed resampling of single slice RGB images
  • Fixed incorrect reading of the AmiraMesh header for the fuse mode of the Chop tool
  • [Programming] moved mibController.connImaris to mibModel.connImaris
  • [Programming] updated syntax of mibImage.clearMask

    Version 2.12 18.09.2017
    Matlab Windows, 64bit, R2017a
  • Added a new tool to detect a frame around images (Menu->Image->Tools for images->Select image frame...)
  • Added the auto-update mode for the Graphcut segmentation
  • Added possibility to count annotations in the List of annotations window: Segmentation panel->Annotations->Annotation list->Right mouse click over the table with annotations
  • Added export of selected annotations to Amira as landmark points or to Matlab: Segmentation panel->Annotations->Annotation list->Right mouse click over the table with annotations
  • Added saving of annotations to Amira landmarks format (Segmentation panel->Annotations->Annotation list->Save)
  • Added sorting of annotations in the Annotation list window: Segmentation panel->Annotations->Annotation list->Sort table
  • Added possibility to remove branches during morphological thinning: Menu->Selection->Morphological 2D/3D opetations->Thin
  • Added clipping with Mask for image dilation
  • Added shift of annotations during resampling
  • [Programming] Added material names parameter to call of mibImage.createModel function
  • Improved performance when selecting objects in the Get Statistics window in the the Add and Replace modes
  • Improved resizing of the Log List window
  • Improved update of the Graphcut window when switching datasets
  • Modified use of the E key shortcut, now it toggles between two recently selected materials
  • Fixed reading of metadata for MRC files
  • Fixed loading of models when only the z-dimension is mismatched
  • Fixed use of the block mode, when options .x, .y, .z are present in mibModel.getDataXD/mibModel.setDataXD functions
  • Fixed erode and dilate for elongated kernels
  • Fixed backup before interpolation for the YZ and XZ orientations
  • Fixed access to the Class Reference documentation (Menu->Help->Class Reference)
  • Fixed import of annotations that are in a wrong orientation
  • Fixed export of TIF images in the sequential mode

    Version 2.1 01.06.2017
    Matlab Windows, 64bit, R2017a MacOS, 64bit, R2017a
  • Added materials with 65535 maximal number of materials
  • Added export to Excel for non-PC platforms via xlwrite: Generate XLS(X) files without Excel on Mac/Linux/Win
  • Added automatic mode for interpolation of images shown in the Image View panel. When magnification is 100% or higher MIB is using the nearest method, otherwise bicubic
  • Added Median3D filter to the Image Filters panel (R2017a and newer)
  • Added running average correction to the Alignment tool
  • Added to the Statistics dialog generation of new models, where each object has its own index
  • Added find and select material under the mouse cursor using the ^ Ctrl+F shortcut
  • Added pasting of selection to all layers (Menu->Selection->Selection to buffer->Paste to all slices (Ctrl+Shift+V)
  • Added indication of material index under the mouse cursor to the Pixel info of the Path panel
  • Added possibility to save models for MIB version 1 (File->Models->Save model as...->Matlab format for MIB ver. 1 (*.mat))
  • Modified use of ^ Ctrl+C/^ Ctrl+V, now the stored dataset can be pasted to any other dataset in MIB assuming that the dataset have the same width/height. As result storedSelection property of mibImage class has been moved to mibModel class
  • Fixed export of models and masks to another MIB dataset for the compiled version
  • Fixed singleton running of MIB, now it is possible to have several instances of MIB run in parallel

    Version 2.01 11.04.2017
    Matlab Windows, 64bit, R2017a
  • Added selection of the model type to Menu->Models->Type and removed it from the Preferences dialog
  • Added 'Recalculate selected measurements' function to the Measure tool to recalculate distances and image intensities
  • Added possibility to exclude black or white intensities when using the contrast normalizaton of Z-stacks (Menu->Image->Contrast->Normalize layers->Z stack)
  • Added imresize3 function to resample datasets with R2017a (40-50% faster)
  • Added calculation of annotation labels occurrence in the Stereology tool
  • Moved mibView.disableSegmentation to mibModel.disableSegmentation
  • Bug fixes

    Version 2.00 20.03.2017 /2.001

  • With release 2.0 MIB has been rewritten to utilize Controller-View-Model architecture, which brings stability and ease of future development. However, because of that, the system requirements for Matlab were increased and MIB2 is only available for Matlab R2014b and older (due to continuous development of Matlab, the most recent release is always recommended)
  • Added offset shift for the rechop mode (ver. 2.001)
  • Big fixes (ver. 2.001)

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