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MIB version 2
Actual versions
MIB MATLAB 2.82 [12.04.2022]
MIB Windows 2.82 [12.04.2022]
MIB Mac 2.82 [12.04.2022]
MIB Linux 2.81 [14.10.2021]
If you have a valid MATLAB license it is recommended to use MIB for MATLAB environment version!


To download MIB please select the distribution and press the corresponding button on the right:
  • MATLAB version - we recommend to use this option, requires MATLAB license
  • Academic Standalone for Windows - MIB compiled for MATLAB R2021b
  • Academic Standalone for MacOS - MIB compiled for MATLAB R2021b for Mac OS
  • Academic Standalone for Linux - MIB compiled for MATLAB R2019b for Linux
  • GitHub - MIB source code on GitHub, virtually identical to the MATLAB version above
Please look here for installation details.


    Version 2.82 (12.04.2022)
    The standalone versions of MIB-Win and MIB-Mac come with R2021b, while MIB-Linux comes with R2019b
  • 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


    Version 2.81 (14.10.2021)
    MATLAB Windows, 64bit, R2021b
    The standalone versions of MIB-Win and MIB-Mac come with R2021b, while MIB-Linux comes 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


Click to access archive with previous versions of MIB2

MIB version 1 [LEGACY RELEASE]


    Version 1.305 23.12.2016 [LEGACY RELEASE]
  • Improved and simplified the Segmentation panel
  • Added list of recent directories
  • Added "Mask_" prefix to filename when saving masks
  • Added "FirstAxisLength" and "SecondAxisLength" properties to the Get Statistics dialog for calculation of exact lengths of the objects (ver 1.302)
  • Added default state of the link channels checkbox to selected in the Display adjustment dialog (ver 1.302)
  • The contrast normalization over selected areas in Z does not require selection of all slices
  • Fix of substructures in Dataset Info dialog
  • Fix of fine-tune checkbox for the freehand mode of the measure tool
  • Improved performance of black-and-white thresholding
  • Fix of add matarial bug (ver 1.303)
  • Fix of export annotations to a file for MacOS (ver 1.303)
  • Fix startup crashes for compiled MIB on some windows configurations (ver 1.304)
  • Update of font size for buttons and popup menus (ver 1.305)
  • Fix of a bug in the masked-based image alignment tool (ver 1.305)




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