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.

BETA RELEASE Version 2.9047 (25.04.2025)

b47

b43

Note! the beta version for Windows was compiled with R2024b

• [b47] Fixed adding a model in the rotated view when the blockMode is on
• [b46] Added the auto-preview checkbox into the Multi rename tool
• [b45] Improved GPU memory handling when using SAM-1/SAM-2; updated documentation
• [b44] Added modification of the Info box into freeline of Measure Tool
• [b43] Added possibility to specify prefixes in the Multi rename tool
• [b42] Fix SAM3 Interactive 3D for 16bit images
• [b41] Added Interactive 3D mode for SAM2
• [b40] Added export and save of the selected material of the model
• [b39] [DeepMIB] Rearrangement of 2.5D Z2C DLv3 networks, bug fixes
• [b38] Added Multi-rename tool for batch renaming of files: plugins->File processing->Multi rename tool
• [b38] Added swap of colors in the model from the segmentation panel
• [b37] Added operations with materials: add, insert, rename, reorder, swap, remove
• [b35] Fixed correct handling of random numbers in the augmentation patches preview
• [b35] Fixed accidental appearance of Deep.AugOpt2D.ImageNoise field in augmentation preferences
• [b35] Added loading of part of dataset using BioFormats reader
• [b34] Added SIFT feature detector for automatic alignment
• [b33] Added a new version of automatic alignment (Automatic feature-based v2)
• [b31] Added option of returning back to a slice: use Alt+scroll wheel to change slice; release Alt to return back to the slice when Alt+scroll wheel was triggered
• [b30] Added shortcuts (Shift+D, Ctrl+D) for two favorite segmentation tools
• [b29] Added presets for segmentation tool (Shift+1/2/3 stored the current state and 1/2/3 restores it)
• [b29] Added warning dialog when loading files, while a model exists
• [b26][DeepMIB] Fixed Explore activations when images for prediction are not under Images directory

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)