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 R2023b
• Academic Standalone for Windows, recent MATLAB - MIB compiled for the recent release of MATLAB
• Academic Standalone for MacOS - MIB compiled for MATLAB R2024a for Mac OS
• Academic Standalone for Linux - MIB compiled for MATLAB R2024a for Linux
• GitHub - MIB source code on GitHub, virtually identical to the MATLAB version above

Please look here for installation details.

Version 2.91 beta 21 (07.01.2025)
• Added Segment-anything-2 and 2.1 models for manual/semi-automatic segmentation
• Added 3D mode for Segment-anything-2 models
• Added new rendering modes for volumes (CinematicRendering, LightScattering) and overlays (LabelOverlay, VolumeOverlay, GradientOverlay) in MIB rendering
• Added use of annotations to perform single landmark point alignment
• Added automatic interpolation of annotations when they added using shift+mouse click
• Added rotation around selected object, ambient and diffuse lights in MIB 3D volume rendering
• Added pattern rename of annotations
• Fixed 3D rendering of the selected material
• [b21] Fixed SAM2 for Linux
• [DeepMIB] Added image downsampling paramter for automatic resizing of images for prediction
• [DeepMIB] Added automatic saving of the custom training plot as PNG

Version 2.9012 (07.08.2024)
Windows, 64bit, R2023b Linux, 64bit, R2024a

• To comply with dependencies the MIB license was updated from GPLv2 to GPLv3
• Added Segment anything (Standard and Microscopy) models for manual/semi-automatic segmentation
• 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 2.5D network architectures for semantic segmentation
• [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, placed 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
• [2.9011] Added "add, +next material" to SAM in the Destination "selection"
• [2.9012] Added currently selected material to move layers in batch processing; fixed indices for adding annotations from statistics; added import of landmarkAscii and landmarkBin from Amira

Click to access archive with previous versions of MIB2

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)