v2.9020 compiled MIB for academic research

The standalone versions of MIB come with R2023b

• To comply with dependencies the MIB license was updated from GPLv2 to GPLv3
• Added Rename materials to batch processing operations
• Added possibility to skip loading of metadata
• Added the Cancel button to the progress bar upon loading of images
• Added recoloring of materials for models with 65535+ materials
• Added crop of 3D volumes from 2D objects detected using the Get Statistics window
• Added options to change thickness of model and mask contour lines (Menu->File->Preferences->Colors and styles->Contours)
• Added drag and drop *.mask files to the Image view panel to load them
• Added drag and drop *.ann files to the Image view panel or the Segmentation table to load annotations
• Added paste of annotation values from clipboard
• Added auto fill switch to the Selection panel to fill the shapes after use of brush
• Added jitter coordinates option into crop out patches for annotations and objects
• Added [F] template for exporting statistics via batch processing
• Added saving of projects, copy to clipboard and open in file explorer for directories in Menu->File->Rename and Shuffle->Restore
• Added possibility to load measurements (*.measure) from multiple files and added filename to export of measurement in the Excel format
• Added possibility update colors of annotations into the Annotation list window
• Added key shortcuts to zoom in to 100% and fit to view. The shortcuts can be modified using via Menu->File->Preferences->Keyboard shortcuts
• Added key shortcut to rename materials (default F2)
• Added key shortcuts to change the brush size (default [ and ])
• Added possibility to hide the Path and the bottom panels (Selection, View settings, Image filters) via a dropdown menu over the Image view panel
• Added filename identifier when exporting object quantification from the Get Statistics window
• Added filename identifier when exporting annotations to Excel or CSV
• Added "Center-top" and "Center-bottom" locations to Add frame (Menu->Dataset->Transform->Add frame->Provide new width/height)
• Added "Set value" to the batch modify selected annotations (Menu->Models->Annotations->List of annotations)
• Added interpolation operation to the List of Annotations
• Added options to add annotation names and coordinates to filenames when generating patches from annotations
• Added automatic selection of materials from selected rows in the segmentation table for the remove material operation
• Added option to add multiple empty slices using (Menu->Dataset->Slice->Insert empty slice)
• Added selection of colors for materials into the segmentation table (right mouse click->Color scheme)
• Added fusing of a larger model into a smaller dataset crop (Menu->File->Chopped images->Import->Fused...)
• Added possibility to define black and white points lower and higher than the image class allows (Image view panel->Display)
• Added possibility show masks as filled shapes (Menu->File->Preferences->Colors and styles->Masks)
• Added an option to add annotation name when exporting them to PSI format
• Added measurements to Rename and Shuffle
• Added save of models and masks to PNG format
• Added the Threshold button to the BW thresholding tool to start thresholding manually
• Added user tiers
• Improved calculation of DistanceMaps in 3D for isotropic voxels
• Changed usage of the Object picker tool, now the object pick is based on the selected row in the segmentation table
• Changed how the object id values are displayed in the Statistics window, now they show the real indices of the detected objects
• Fixed Add frame when dX or dY is 0
• Fixed Resize of models that have more than 255 materials
• Updated Bio-Formats to 7.2.0
• [DeepMIB] Added training using Multi-GPU configuration
• [DeepMIB] Added prediction using Multi-GPU configuration for the patchwise workflows
• [DeepMIB] Added new dialog to specify augmentation settings
• [DeepMIB] Added drag-and-drop of *.mibCfg project files into panels of DeepMIB to automatically load the config
• [DeepMIB] Added duplication operation to make a copy of a trained network and its config
• [DeepMIB] Added padding parameter to symmetrically pad the image to eliminate the edge artifacts
• [DeepMIB] Added symmetric padding for prediction using Blocked-image engine to eliminate edge artifacts (R2023a and newer)
• [DeepMIB] Added export of the trained network to TensorFlow format
• [DeepMIB] Added 'MATLAB non-compressed format (range 0-1)' for generating predictions scores in the range from 0 to 1
• [DeepMIB] Added possibility to predict images that are not under Images subfolder (Blocked-mode only)
• [DeepMIB] Added an option to calculate loss excluding Exterior when using the diceCustom segmentation layer
• [DeepMIB] Added sending of email notifications about training progress and when finished
• [DeepMIB] Added preview of a network stored in mibDeep file (Network panel)
• [DeepMIB] Added possibility to mask-away areas without preprocessing (Mask extension: Use 0-s in labels)
• [DeepMIB] Improved handling of directories that are RELATIVE to the project directory
• [DeepMIB] Extended the Evaluate segmentation plot with Class and Dataset metrics

[2.9002] Updated GUI windows
[2.9003] Added mib_prefs_override.mat file to override default settings of MIB, pleased at the same location as mib.m
[2.9004] Fix accidental incompatibility augmentation settings bug in DeepMIB
[2.9005] Added update on zoom of the shown area dimensions for snapshot and movie maker tools
[2.9006] Added usage of a reference slice for contrast normalization
[2.9007] Fixed import of older versions of DeepMIB configs
[2.9008] Fixed selection of 2D objects in Get Statistics; compatibility fix with R2019b
[2.9009] Added SAM for YZ and XZ orientations
[2.9010] Fix of file check during transfer learning

Full Changelog: v2.9009...v2.9009

v2.84 compiled MIB for academic research

• Added Example datasets: Menu->File->Example datasets
• Added new 3D Volume renderer (at the moment only for MATLAB version): Menu->File->Render volume->MIB rendering
• Added alignement of datasets without loading using the Automatic feature-based mode
• Added white balance correction (Menu->Image->Tools for images->White balance correction)
• Added linking of views
• Added export images to OME-TIFF 5D formatMenu->File->Save image as...
• Added modification of annotation size to settings in the Annotation list window
• Added [F] template for saving images to Batch Processing
• Added showWaitbar option to Batch Processing of DIRLOOPs
• Added resizing of panels to the batch processing dialog
• Added erosion of models and erosion with parallel processing
• Added dilation of models
• Added calculation of DistanceMaps relative to model, masks, or selections (Menu->Image->Image Filters->Basic image filtering->DistanceMap)
• Added basic mathematical operations (add, subtract, multiply, divide to image filters (Menu->Image->Image Filters->Basic image filtering->MathOps)
• Added destination "Current" to the Intensity Projection tool (Menu->Image->Tools for Images->Intensity projection)
• Updated Bio-Formats to 6.11.0 (please delete the old bioformats_package.jar from MIB\ImportExportTools\BioFormats)
• Updated Plugins->TripleAreaIntensity to highlight the connected objects using the Mask layer
• Fixed bug in the shape interpolation method seen in some configuration of shapes (thanks to Aapo Tervonen, PhD, University of Jyväskylä)
• Fixed slow update of selected directory in CropObjects to file dialog
• Fixed application of MorphOps for images when the active container of MIB has been changed
• Fixed loading of some jpg files due to multiple ImageDescription tags
• [DeepMIB] Added prediction of 3D stacks with 2D models
• [DeepMIB] Added possibility to specify patch size during augmentation preview
• [DeepMIB] Added 'DeepLabV3 Xception' and 'DeepLabV3 Inception-ResNet-v2' for MATLAB version of MIB
• [DeepMIB] Added swish activation layer as one of available options
• [DeepMIB] Added a function to balance classes for large rasters (Options tab->Tools->Balance classes)
• [DeepMIB] Added network preview for the deployed version
• [DeepMIB] Added saving of the custom training plot as an image to a file
• [DeepMIB] Added scaling of the loss function plot upon right mouse click
• [DeepMIB] Fixed generation of score maps for the Legacy mode

v2.83 compiled MIB for academic research

Compiled MIB version 2.83 for Academic research (19.06.2022).
compiled with R2021b

• Added generation of image 2D and 3D patches around annotation labels
• Added possibility to load part of the dataset for TIF files (right click over selected filenames->Load part of the dataset (AM and TIF))
• Added Info field to measurements to supplement them with additional information (Menu->Tools->Measure length->Measure tool)
• Added the "show prompt" option to the Annotations tool (Segmentation panel->Annotations->show prompt)
• Added [InheritLastDIR] tag to inherit directory name from DIR LOOP when saving images using the Protocol organizer
• Added "end" tag to the crop operation for the Protocol organizer
• Added Drag-and-drop model files to the Segmentation table to load them
• Correction of pixel size for pyramidal formats when levels are not multiplied by factor of 2
• Fixed loading of partial AM files, when step was set to 1
• Fixed loading of TIF files with YCbCr color space
• Updated Bio-Formats to 6.10.0
• [DeepMIB] Rearranged Architecture into Workflow and Architecture parameters
• [DeepMIB] Optimized to work without preprocessing of images
• [DeepMIB] Added blockedImage mode and set it as default processing engine
• [DeepMIB] Added dynamic masking for the blockedImage processing mode
• [DeepMIB] Added 2D Patch-wise mode to process images in patches
• [DeepMIB] Added Resnet18, Resnet50, Resnet101, Xception networks for the patch-wise mode
• [DeepMIB] Added alternative arrangement of files for 2D Patch-wise mode where each class is stored in its own directory
• [DeepMIB] Added "Load models" to the Options tab to skip loading of images when they are already preloaded
• [DeepMIB] Added possibility to specify frequency of saving checkpoint networks (R2022a or newer)
• [DeepMIB] Added percentage parameter to the overlapping tiles mode
• [DeepMIB] Added possibility to select a single augmentation to preview
• [DeepMIB] Added new 3D augmentations reaching 18 operations
• [DeepMIB] Added DeepLabV3-Resnet50 to 2D semantic segmentation (MATLAB MIB only)
• [DeepMIB] Fixed preview of some patches and contrast stretch in Activation Explorer
• Bug fixes

v2.82 compiled MIB (Win, Mac) for academic research

Compiled MIB version 2.82 for Academic research (12.04.2022).
Windows and Mac versions were compiled with R2021b

• Added generation of kymographs to Measure tool
• Added indexing of objects in a model to generate a new model, where each object has own index (Menu->Models->Convert type->Indexed objects)
• Added main window keypress callbacks to Statistics, Measure tools, Image adjustments, Dataset Info, Log, Batch processing, Make movie, Snapshot, Crop, Resample, Bounding box, Image filters, Image arithmetics, MorphOps, Image MorphOps, Graphcut, Stereology, Object separation, Global black-and-white thresholding, Watershed segmentation, Supervoxel classifier, Membrane detection; when these tools are in focus, the key shortcuts of the main window are triggered
• Added reading of pixel size from Zeiss SmartSEM and Atlas TIF files
• Added automatic extraction of metadata from Zeiss Atlas and SmartSEM TIF files (Menu->Plugins->File processing->Image converter: TIF->XML)
• Added "Selected files in Directory contents" option into "Load and combine images" option of the Batch processing tool
• Added 'ndpi' format to the list of BioFormats extensions
• Added new options for faster placing measurements (Menu->Tools->Measure length->Measure tool)
• Added Esc key shortcut to stop placing measurements
• Added Shift+Alt+RMB key shortcut to pan the image
• Fixed loading of the selected series from a container file using BioFormats
• Fixed starting of Fiji volume viewer directly from MIB
• Fixed usage of Shift+LMB operations
• Fixed of delete operation of a single tree in 3D lines
• Fixed resize in batch processing mode, when z-value was kept fixed with the percentageXY option
• Bug fixes
• [DeepMIB] Added 2D DeepLabV3-Resnet18 architecture for semantic segmentation
• [DeepMIB] Added selection of the output format as MIB Model or TIF
• [DeepMIB] Added possibility to return the trained network with the best validation loss (Training settings, requires R2021b or newer)
• [DeepMIB] Added indicator of the iteration with the selected network and rendering of training and validation final loss values that were missing on the progress training plot
• [DeepMIB] Fixed probability of generation of an augmented patch
• [MCcalc] Added calculation of areas and average min thickness for the main objects
• [MCcalc] Added calculation contacts between objects of the same material

v2.81 compiled MIB (Win, Mac, Linux) for academic research

Compiled MIB version 2.81 for Academic research (14.10.2021).
Windows and Mac versions were compiled with R2021b, while Linux with R2019b

• Added contrast adjustment, when 16-bit is converted to 16-bit
• Added import of annotations from CSV files (Segmentation table->Annotations->Annotation list->Load
• Added conversion of annotations to the mask layer (Annotations->Annotation list->List of annotations->Convert selected annotations to Mask)
• Added save of models to mibCat categorical format (Menu->Models->Save model as)
• Added automatic closing of all windows in Fiji when stopping FijiConnect
• Added information about "Call4Help" sessions (Menu->Help->Call for help)
• Fixed a bug with generation of grids in the Stereology tool
• Fixed automatic feature based alignment, when the Selection is disabled
• Updated Bio-Formats to 6.7.0
• [DeepMIB] added counting of labels in model files (Options->Count labels)
• [DeepMIB] fixed bug with selection of 'Multi GPU' for prediction

v2.802 compiled MIB (Win) for academic research

Compiled MIB version 2.802 for Academic research to be used without Matlab installation
(02.06.2021).
The standalone compiled version of MIB comes with R2021a
For full release notes check:
http://mib.helsinki.fi/downloads.html

version 2.802

• fix of crash in compiled application when starting color chooser
• fix when select directories dialog sends main MIB window to top
• fix of ExternalDirectories in preferences initialization

MIB Beta v2.716

Beta version of MIB for Matlab and Windows

v2.702 compiled MIB (Win, Mac, Linux) for academic research

Small update targeted for Linux mostly, includes compiled version for Linux

Compiled MIB version 2.702 for Academic research to be used without Matlab installation
(01.02.2021).
The standalone compiled version of MIB comes with R2019b

• Added DeepMIB for training and prediction of datasets using deep convolutional networks (Menu->Tools->Deep learning segmentation)
• Added 2D Elastic Distortion filter (Menu->Image->Image Filters)
• Added resizing of the Image Arithmetics window
• Added selection of a seed for random generator for Rename and Shuffle tool
• Fixed issues with importing of chopped cropped datasets

MIB 2.712 BETA

Many changes with DeepMIB
Fixes for MacOS Catalina users
Re-worked preference system (the preferences of version 2.711 and newer are not compatible with older versions of MIB! Delete mib.mat file with preferences if the older versions of MIB are used after this beta)
and much, much, more...

MIB Matlab 2.712
MIB Windows 2.712 (18.02.2021)

MIB compiled

Compiled MIB version 2.651 for Windows to be used without Matlab installation
(25.04.2020). For the Mac version please use version 2.65.
The deployed version of MIB comes with R2019b instead of R2017a

• Added smoothing of multiple materials of models via batch processing
• Fixed definition of the starting point for the Membrane ClickTracker tool
• Fixed setData method for specific materials of the model