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# Hitrory of Releases

Back to MIB | Getting started | Current release notes

This page lists the release history for Microscopy Image Browser (MIB), detailing new features, improvements, and fixes across versions.
For the latest updates, visit MIB website or check the current release notes.

2.9012 / 24.07.2024 (SAM segmentation, Multi-GPU training, 2.5D CNNs)

- 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 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
- 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 via a dropdown menu
- Added filename identifier when exporting object quantification
- Added filename identifier when exporting annotations to Excel or CSV
- Added "Center-top" and "Center-bottom" locations to Add frame
- Added "Set value" to the batch modify selected annotations
- Added interpolation operation to the List of Annotations
- Added options to add annotation names and coordinates to filenames when generating patches
- Added automatic selection of materials from selected rows in the segmentation table
- Added option to add multiple empty slices
- Added selection of colors for materials into the segmentation table
- Added fusing of a larger model into a smaller dataset crop
- Added possibility to define black and white points lower and higher than the image class
- Added possibility show masks as filled shapes
- Added an option to add annotation name when exporting 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
- Added user tiers
- Improved calculation of DistanceMaps in 3D for isotropic voxels
- Changed usage of the Object picker tool
- Changed how the object id values are displayed in the Statistics window
- 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
- [DeepMIB] Added new dialog to specify augmentation settings
- [DeepMIB] Added drag-and-drop of "mibCfg" project files
- [DeepMIB] Added duplication operation to make a copy of a trained network
- [DeepMIB] Added padding parameter to symmetrically pad the image
- [DeepMIB] Added symmetric padding for prediction
- [DeepMIB] Added export of the trained network to TensorFlow format
- [DeepMIB] Added 'MATLAB non-compressed format (range 0-1)'
- [DeepMIB] Added possibility to predict images that are not under Images subfolder
- [DeepMIB] Added an option to calculate loss excluding Exterior
- [DeepMIB] Added sending of email notifications about training progress
- [DeepMIB] Added preview of a network stored in mibDeep file
- [DeepMIB] Added possibility to mask-away areas without preprocessing
- [DeepMIB] Improved handling of directories
- [DeepMIB] Extended the Evaluate segmentation plot
- [2.9002] Updated GUI windows
- [2.9003] Added 'mib_prefs_override.mat' file to override default settings
- [2.9004] Fix accidental incompatibility augmentation settings bug
- [2.9005] Added update on zoom for snapshot and movie maker tools
- [2.9006] Added usage of a reference slice for contrast normalization
- [2.9007] Fixed import of older DeepMIB configs
- [2.9008] Fixed selection of 2D objects in Get Statistics
- [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
- [2.9012] Added currently selected material to move layers; fixed indices for annotations; added import of landmarkAscii and landmarkBin

2.84 / 09.12.2022 (new 3D viewer and HDD alignment)

- Added Example datasets
- Added new Volume renderer
- Added export images to OME-TIFF 5D format
- Added alignment of datasets without loading
- Added white balance correction
- Added modification of annotation size
- Added [F] template for saving images
- Added showWaitbar option to Batch Processing
- Added resizing of panels to batch processing
- Added erosion of models with parallel processing
- Added dilation of models
- Added linking of views
- Added calculation of DistanceMaps relative to model, masks, or selections
- Added basic mathematical operations to image filters
- Added destination "Current" to Intensity Projection
- Updated Bio-Formats to 6.11.0
- Updated Plugins->TripleAreaIntensity to highlight connected objects
- Fixed bug in shape interpolation
- Fixed slow update of selected directory
- Fixed application of MorphOps
- Fixed loading of some jpg files
- [DeepMIB] Added prediction of 3D stacks with 2D models
- [DeepMIB] Added possibility to specify patch size during augmentation
- [DeepMIB] Added 'DeepLabV3 Xception' and 'DeepLabV3 Inception-ResNet-v2'
- [DeepMIB] Added swish activation layer
- [DeepMIB] Added a function to balance classes
- [DeepMIB] Added network preview for deployed version
- [DeepMIB] Added saving of custom training plot
- [DeepMIB] Added scaling of loss function plot
- [DeepMIB] Fixed generation of score maps

2.831 / 21.06.2022; 2.83 / 19.06.2022 (blockedImage and 2D patch-wise)

- Added generation of image 2D and 3D patches around annotation labels
- Added possibility to load part of the dataset for TIF files
- Added Info field to measurements
- Added generation of pyramidal TIF files
- Added the "show prompt" option to Annotations tool
- Added [InheritLastDIR] tag to inherit directory name
- Added "end" tag to crop operation
- Added Drag-and-drop model files
- [2.831] Added Destination: Current to Crop
- Correction of pixel size for pyramidal formats
- Fixed loading of partial AM files
- Fixed loading of TIF files with YCbCr color space
- [2.831] MATLAB versions compatibility bug fixes
- Updated Bio-Formats to 6.10.0
- [DeepMIB] Rearranged Architecture into Workflow
- [DeepMIB] Optimized to work without preprocessing
- [DeepMIB] Added blockedImage mode
- [DeepMIB] Added dynamic masking
- [DeepMIB] Added 2D Patch-wise mode
- [DeepMIB] Added Resnet18, Resnet50, Resnet101, Xception networks
- [DeepMIB] Added alternative arrangement of files
- [DeepMIB] Added "Load models" to Options tab
- [DeepMIB] Added frequency of saving checkpoint networks
- [DeepMIB] Added percentage parameter to overlapping tiles
- [DeepMIB] Added possibility to select a single augmentation
- [DeepMIB] Added new 3D augmentations
- [DeepMIB] Added DeepLabV3-Resnet50
- [DeepMIB] Fixed preview of patches

2.82 / 12.04.2022 (DeepLabV3, kymographs, key callbacks)

- Added generation of kymographs
- Added indexing of objects in a model
- Added main window keypress callbacks
- Added reading of pixel size from Zeiss SmartSEM
- Added automatic extraction of metadata
- Added "Selected files" option
- Added 'ndpi' format
- Added new options for faster measurements
- Added Esc key shortcut
- Added Shift+Alt+RMB key shortcut
- Fixed loading of selected series
- Fixed starting of Fiji volume viewer
- Fixed usage of Shift+LMB operations
- Fixed delete operation of a single tree
- Fixed resize in batch processing
- Bug fixes
- [DeepMIB] Added 2D DeepLabV3-Resnet18 architecture
- [DeepMIB] Added selection of output format
- [DeepMIB] Added return of trained network
- [DeepMIB] Added indicator of iteration
- [DeepMIB] Fixed probability of augmented patch
- [MCcalc] Added calculation of areas
- [MCcalc] Added calculation contacts

2.81 / 14.10.2021

- Added contrast adjustment for 16-bit
- Added import of annotations from CSV
- Added conversion of annotations to mask
- Added save of models to mibCat format
- Added automatic closing of Fiji windows
- Added information about "Call4Help"
- Fixed bug in Stereology tool
- Fixed automatic feature-based alignment
- Updated Bio-Formats to 6.7.0
- [DeepMIB] Added counting of labels
- [DeepMIB] Fixed bug with Multi GPU

2.802 / 01.06.2021

- Added HDD mode to align datasets
- Added new preference dialog
- Added exclusion of Stretch and Shear peaks
- Added re-ordering of annotations
- Added precision edit box
- Added "Extra depth to show annotations"
- Added saving of models as 2D sequence
- Added Mode filter
- Added "File and Directory operations"
- Added plugin for converting images
- Added plugin detection of contacts
- Added shift of color channels
- Added check for new version
- [DeepMIB] Added selection of GPU/CPU
- [DeepMIB] Added GPU Info window
- [DeepMIB] Added training without preprocessing
- [DeepMIB] Added parallel pre-processing
- [DeepMIB] Added compatibility with TIF and PNG
- [DeepMIB] Added masking
- [DeepMIB] Added 19 2D augmentation operations
- [DeepMIB] Added configurable preview
- [DeepMIB] Added configurable preview during training
- [DeepMIB] Added selection of activation layers
- [DeepMIB] Added Transfer Learning
- [DeepMIB] Added setting of mini-batch size
- [DeepMIB] Added export of prediction scores
- [DeepMIB] Added Sørensen-Dice similarity
- [DeepMIB] Added export to CSV
- [DeepMIB] Added export to ONNX format
- Updated reading of NRRD files
- Updated export statistics
- Updated Bio-Formats to 6.6.1
- Updated for MATLAB R2021a
- Fixed missing "Add to" checkbox
- Fixed loading of AM files
- Fixed preview behavior
- Fixed 3d backup operation
- Fixed vertical flip of MRC datasets
- Replaced quantile function
- Bug fixes

2.70 / 18.05.2020

- Added Deep MIB for training
- Added 2D Elastic Distortion filter
- Added resizing of Image Arithmetics
- Added selection of a seed
- Fixed issues with importing

2.66 / 25.04.2020

- Added direct conversion from Mask to Model
- Added drag-and-drop for *.model files

2.651 / 25.04.2020

- Added smoothing of multiple materials
- Fixed definition of starting point
- Fixed setData method

2.65 / 23.03.2020

- Added Drag and drop files
- Added dialog with 30 new image filters
- Added dataset alignment using AMST
- Added wound healing assay
- Added transformation of Z to C
- Added additional options to batch processing
- Added backup of mibImage class
- Added full backup for dataset operations
- Added squeezing of material indices
- Added a new key shortcut ('n')
- Added saving snapshots in PNG
- Added measurements to restore shuffled datasets
- Updated resampling
- Updated Bio-Formats to 6.4.0
- Swapped Log and Info buttons
- Tweaked names of plugins
- Optimized handling of Java classes
- Plugins: Surface Area 3D
- Plugins: Spacial Control Points
- Plugins: Cell Wall Thickness

2.601 / 04.11.2019

- Deployed version with R2019b
- Added Batch mode
- Added visualization of models
- Added Drag & Drop materials
- Added alignment of color channels
- Added content-aware fill
- Added debris removal tool
- Added ORB points
- Added correction for instant jumps
- Added export of quantitation results
- Added export to CSV
- Added copy to clipboard
- Added batch modification
- Added 4D options
- Added calculation of quantile
- Added "Ctrl+e" key shortcut
- Added export of graphs
- Rewritten Image arithmetics
- Updated use of xlswrite
- Updated data conversion
- Updated Bio-Formats to 6.2.1
- Bug fixes
- Added export of annotations to CSV

2.51 / 13.03.2019

- Added automatic global thresholding
- Added selection of materials
- Added focus stacking
- Added saving of HDF5
- Added saving of AmiraMesh
- Added display of orthoslice
- Added tip of the day
- Added H-maxima and H-minima
- Added Single Mask object
- Added export of supervoxels
- Improved performance
- Improved Image arithmetics
- Updated BioFormats reader
- Updated sorting
- Fixed initialization of 3D rendering
- Fixed pixel size
- Fixed adding icons

2.501 / 21.12.2018

- Added swap slices option
- Fixed rendering of combined image
- Fixed Copy Slice

2.50 / 17.12.2018

- Added hardware accelerated 3D rendering
- Added automatic image alignment
- Added 20 distinct colors palette
- Added center point marker
- Added shuffling of annotations
- Added delete multiple materials
- Added change default filters
- Added contrast normalization
- Added fuse of annotations
- Added auto removal of spaces
- Added loading of masks
- Added alternative way to specify frame
- Improved Lasso mode
- Updated Bio-Formats to 5.9.2
- Fixed compatibility issues
- Fixed bug in object separator
- Fixed scale bar instructions
- Fixed update of color channel
- Fixed conversion to grayscale
- Fixed insert of datasets
- Fixed scroll wheel
- Fixed combine files
- Fixed missing values
- Fixed computation of statistics
- Fixed cropping of selection
- Fixed alignment

2.40 / 31.08.2018

- Added virtual mode
- Added shift of annotations
- Added Segment All function
- Improved performance
- Updated BioFormats to 5.9.1
- Bug fixes

2.302 / 18.05.2018 (03.07.2018)

- Added Lines3D class
- Added Image arithmetics dialog
- Added Rename and Shuffle tool
- Added alignment using landmarks
- Added modification of Imaris path
- Added calculation of 3D skeleton
- Added export to MATLAB VolumeViewer
- Added quantitation of objects
- Added insert an empty slice
- Added recentering the view
- Added export of TransformationMatrix
- Fix of cropping objects
- [2.301] Added filter for filenames
- [2.302] Fixed export of 3D lines
- [2.302] Fixed recalculation of pixels

2.22 / 16.03.2018

- Added value field for annotations
- Added deep neural network denoising
- Added Simplify button
- Added rendering with Imaris
- Added rendering snapshots
- Added rendering of annotations
- Added Get Statistics
- Added external BMxD filters
- Added Add Frame tool
- Added renaming of annotations
- Improved movie rendering
- Updated Image Filter panel
- Fix of error in Morph Closing
- Fix callback
- Fix of opening of AmiraMesh

2.211 / 21.12.2017

- Updated TripleAreaIntensity plugin
- Fix, replaced contains with ismember
- Fix of lost key press callbacks
- Fix of loading hdf5 datasets
- Minor bug fixes

2.21 / 04.12.2017

- Added model with 4294967295 materials
- Improved object picker
- Fix compiling of certain function
- Fix of 'Fix selection to material'
- Fix connection to Omero

2.20 / 14.11.2017

- Added 3D Grid mode to Graphcut
- Added denoise of image
- Added export annotations to Imaris
- Added possibility to skip intensity profiles
- Added buttons to magnify snapshots
- Added reading of material names
- Added insert of dataset
- Added utilization of block mode
- Rearranged Graphcut, Watershed
- Updated Crop tool
- Updated calculation of curve lengths
- Updated connection to Imaris
- Updated BioFormats to 5.7.1
- Updated inputdlg
- Updated measure line/freehand
- Fixed disabling of selection
- Fixed movement of measurements
- Fixed recalculation of voxels
- Fixed resampling
- Fixed incorrect reading
- Moved mibController.connImaris

2.12 / 18.09.2017

- Added tool to detect frame
- Added auto-update mode
- Added possibility to count annotations
- Added export of selected annotations
- Added saving of annotations
- Added sorting of annotations
- Added remove branches
- Added clipping with Mask
- Added shift of annotations
- Added material names parameter
- Improved performance
- Improved resizing
- Improved update of graphcut
- Modified use of 'E' key
- Fixed reading of metadata
- Fixed loading of models
- Fixed use of block mode
- Fixed erode and dilate
- Fixed backup before interpolation
- Fixed access to Class Reference
- Fixed import of annotations
- Fixed export of TIF images

2.10 / 01.06.2017

- Added materials with 65535 materials
- Added export to Excel
- Added automatic mode for interpolation
- Added Median3D filter
- Added generation of new models
- Added running average correction
- Added find and select material
- Added pasting of selection
- Added indication of material index
- Added possibility to save models
- Modified use of Ctrl+C/Ctrl+V
- Fixed export of models
- Fixed singleton running

2.01 / 11.04.2017

- Added selection of model type
- Added 'Recalculate selected measurements'
- Added possibility to exclude intensities
- Added imresize3 function
- Added calculation of annotation labels
- Moved mibView.disableSegmentation

2.00 / 20.03.2017 Official Release, 2.002 (02.04.2017)

- Rewritten to utilize Controller-View-Model
- Added "Copy to clipboard"
- Added adaptive black and white thresholding
- Many other improvements
- Added offset shift
- Renamed Area to Volume
- Bug fixes

Back to MIB | Getting started | Current release notes