Microscopy Image Browser 2 (MIB2)
- Support 2D-4D datasets (x,y,c,z,t)
- Up to 9 simultaneously opened datasets
- Bounding box for each dataset
- Extendible via plugins
- Log of performed actions
- Customizable undo system
- Customizable keyboard shortcuts
- Colorblind friendly color schemes
- Regions of interests
- Virtual stacking mode for working with datasets that are larger than available memory
- Batch processing mode
- Direct import/export with Matlab , Fiji , Imaris and system clipboard
- Direct import from Omero server and URL links
- Load and save to TIF, Amira Mesh, JPG, Fiji BigDataViewer, HDF5, MRC, NRRD, PNG formats
- Load up to 100 different image and video formats
- Microsoft Excel (export) for quantification
- Rename and shuffle tool for unbiased classification and segmentation
- Objects: Area (2D/3D)
- Objects: ConvexArea (2D)
- Objects: Curve Length (2D, pixels and image units)
- Objects: Eccentricity (2D)
- Objects: Equatorial Eccentricity (3D)
- Objects: Equiv Diameter (2D)
- Objects: Euler number (2D)
- Objects: Extent (2D)
- Objects: Filled area (2D/3D)
- Objects: Holes area (2D/3D)
- Objects: Length between end points (2D/3D)
- Objects: Major axis length (2D/3D)
- Objects: Meridional Eccentricity (3D)
- Objects: Orientation (2D)
- Objects: Perimeter (2D)
- Objects: Second axis length (2D/3D)
- Objects: Solidity (2D)
- Objects: Third axis length (3D)
- Intensity: Correlation (2D/3D)
- Intensity: Maximal (2D/3D)
- Intensity: Mean (2D/3D)
- Intensity: Minimal (2D/3D)
- Intensity: Standard deviation (2D/3D)
- Intensity: Sum (2D/3D)
- Angles
- Caliper
- Circle, radius
- Freehand distance and intensity profile
- Linear distance and intensity profile
- Polyline distance and intensity profile
- Stereology
- Wound healing assay
- 3D ball (3D)
- 3D lines (3D)
- Annotations with values
- Brush tool (2D)
- Brush tool for 2D superpixels (SLIC , Watershed )
- Black and White Thresholding tool (global, local, adaptive; 2D/3D)
- Deep convolutional neural networks for train and prediction
- Dilate (2D/3D, difference)
- Drag & Drop
- Erode (2D/3D, difference)
- Fill holes (2D/3D)
- Frame selection tool
- Frangi tubular filter (2D/3D)
- Graphcut based semi-automatic segmentation(2D/3D) ,
- Lasso tool (2D/3D)
- Magic Wand tool (2D/3D)
- Membrane Click Tracker tool (2D/3D)
- Morphological operations (branch points, diagonal fill, end points, skeleton, spur, thin, ultimate erosion)
- Object Picker (2D/3D)
- Quantification Filtering (2D/3D)
- Random Forest Classifier (2D/3D)
- Shape and Line Interpolation (3D)
- Smooth (2D/3D)
- Spot tool (2D/3D)
- Watershed for automatic image segmentation and object separation (2D/3D)
- 3D ball (3D)
- 3D lines (3D)
- Annotations with values
- Brush tool (2D)
- Brush tool for 2D superpixels (SLIC , Watershed )
- Black and White Thresholding tool (global, local, adaptive; 2D/3D)
- Deep convolutional neural networks for train and prediction
- Dilate (2D/3D, difference)
- Drag & Drop
- Erode (2D/3D, difference)
- Fill holes (2D/3D)
- Frame selection tool
- Frangi tubular filter (2D/3D)
- Graphcut based semi-automatic segmentation(2D/3D) ,
- Lasso tool (2D/3D)
- Magic Wand tool (2D/3D)
- Membrane Click Tracker tool (2D/3D)
- Morphological operations (branch points, diagonal fill, end points, skeleton, spur, thin, ultimate erosion)
- Object Picker (2D/3D)
- Quantification Filtering (2D/3D)
- Random Forest Classifier (2D/3D)
- Shape and Line Interpolation (3D)
- Smooth (2D/3D)
- Spot tool (2D/3D)
- Watershed for automatic image segmentation and object separation (2D/3D)
- Add frame around the dataset
- Alignment
- Brightness, Contrast, Gamma adjustments
- Chop and re-chop large dataset to smaller volumes
- Content-aware fill
- Contrast-limited adaptive histogram equalization
- Color mode change (depth, color type)
- Color channel operations (add, copy, delete, invert, rotate, shift, swap)
- Crop , Resize , Flip , Rotate , Transpose
- Crop 2D/3D objects to files
- Debris removal
- Image arithmetics
- Image filters
- Intensity normalization in Z/T (complete slice, masked areas, background shift)
- Intensity replacement within selected areas
- Invert
- Manipulations with slices: insert, copy, delete
- Intensity projections and focus stacking
- Morphological operations
- Orthoslices (XY, ZX, ZY planes)
- Volume Rendering (hardware)
- Volume Rendering (software)
- Models with Matlab isosurfaces
- Models and volumes with Fiji 3D viewer
- Models and volumes with Imaris
- Export models to IMOD
- Export models to Amira
- Export models to 3D Slicer
- Export models and volumes to Matlab Volume Viewer
- Export models in STL format
Cite As
Ilya Belevich (2024). Microscopy Image Browser 2 (MIB2) (https://github.com/Ajaxels/MIB2), GitHub. Retrieved .
Belevich, Ilya, et al. “Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets.” PLOS Biology, vol. 14, no. 1, Public Library of Science (PLoS), Jan. 2016, p. e1002340, doi:10.1371/journal.pbio.1002340.
Belevich, Ilya, and Eija Jokitalo. DeepMIB: User-Friendly and Open-Source Software for Training of Deep Learning Network for Biological Image Segmentation. Cold Spring Harbor Laboratory, July 2020, doi:10.1101/2020.07.13.200105.
MATLAB Release Compatibility
Platform Compatibility
Windows macOS LinuxCategories
- Sciences > Biological and Health Sciences > Biomedical Imaging >
- Sciences > Biological and Health Sciences > Biomedical Imaging > Microscopy >
Tags
Acknowledgements
Inspired by: view3d.m, IMAGEVIEWER, findjobj - find java handles of Matlab graphic objects, 3D Euclidean Distance Transform for Variable Data Aspect Ratio, Region Adjacency Graph (RAG), stlwrite - write ASCII or Binary STL files, maxflow, Viewer3D, export_fig, Hessian based Frangi Vesselness filter, Accurate Fast Marching, Fast/Robust Template Matching, imgaussian, Highly portable JSON-input parser, Jann5s/measuretool, Render RGB text over RGB or Grayscale Image, improved xlswrite.m, xml2struct, struct2xml, Hardware accelerated 3D viewer for MATLAB, mdrohmann/mtocpp, xlwrite: Generate XLS(X) files without Excel on Mac/Linux/Win, drifty_shifty_deluxe.m, regionprops3
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Classes
Classes/@Labels
Classes/@Lines3D
Classes/@PoolWaitbar
Classes/@ToggleEventData
Classes/@mibAboutController
Classes/@mibAlignmentController
Classes/@mibAnnotationsController
Classes/@mibBatchController
Classes/@mibBoundingBoxController
Classes/@mibChildView
Classes/@mibChopDatasetController
Classes/@mibController
Classes/@mibCropController
Classes/@mibCropObjectsController
Classes/@mibDatasetInfoController
Classes/@mibDebrisRemovalController
Classes/@mibDeepController
Classes/@mibDragNDropControl
Classes/@mibExternalDirsController
Classes/@mibGraphcutController
Classes/@mibHistThresController
Classes/@mibImage
Classes/@mibImageAdjController
Classes/@mibImageArithmeticController
Classes/@mibImageFiltersController
Classes/@mibImageMorphOpsController
Classes/@mibImageSelectFrameController
Classes/@mibImageUndo
Classes/@mibImportOmeroController
Classes/@mibKeyShortcutsController
Classes/@mibLines3DController
Classes/@mibLogListController
Classes/@mibMakeMovieController
Classes/@mibMeasure
Classes/@mibMeasureToolController
Classes/@mibMembraneDetectionController
Classes/@mibModel
Classes/@mibMorphOpsController
Classes/@mibObjSepController
Classes/@mibPreferencesAppController
Classes/@mibPreferencesController
Classes/@mibRandomDatasetController
Classes/@mibRandomRestoreDatasetController
Classes/@mibRechopDatasetController
Classes/@mibResampleController
Classes/@mibRoiRegion
Classes/@mibSnapshotController
Classes/@mibStatisticsController
Classes/@mibStereologyController
Classes/@mibSupervoxelClassifierController
Classes/@mibTipsAppController
Classes/@mibTipsController
Classes/@mibUpdateCheckController
Classes/@mibView
Classes/@mibVolRenAppController
Classes/@mibVolRenAppViewerController
Classes/@mibVolRenController
Classes/@mibWatershedController
Classes/@mibWhiteBalanceController
Classes/@mibWoundHealingAssayController
Classes/@volrenAnimationController
Development/mibPluginGUI_ver1
Development/mibPluginGUI_ver2_Batch_compatible
Development/mibPluginGUI_ver3_appDesigner
Development/mibPlugin_withoutGUI
GuiTools
GuiTools/volren
ImportExportTools
ImportExportTools/Amira
ImportExportTools/BioFormats
ImportExportTools/BioFormats/private
ImportExportTools/Fiji
ImportExportTools/HDF5
ImportExportTools/IMOD
ImportExportTools/IMOD/@ImodChunk
ImportExportTools/IMOD/@ImodChunk/private
ImportExportTools/IMOD/@ImodContour
ImportExportTools/IMOD/@ImodContour/private
ImportExportTools/IMOD/@ImodMesh
ImportExportTools/IMOD/@ImodMesh/private
ImportExportTools/IMOD/@ImodModel
ImportExportTools/IMOD/@ImodModel/private
ImportExportTools/IMOD/@ImodObject
ImportExportTools/IMOD/@ImodObject/private
ImportExportTools/IMOD/@MRCImage
ImportExportTools/IMOD/@MRCImage/private
ImportExportTools/IMOD/Visualization
ImportExportTools/Imaris
ImportExportTools/Imaris/@IceImarisConnector
ImportExportTools/MatTomo/@ImodChunk
ImportExportTools/MatTomo/@ImodChunk/private
ImportExportTools/MatTomo/@ImodContour
ImportExportTools/MatTomo/@ImodContour/private
ImportExportTools/MatTomo/@ImodMesh
ImportExportTools/MatTomo/@ImodMesh/private
ImportExportTools/MatTomo/@ImodModel
ImportExportTools/MatTomo/@ImodModel/private
ImportExportTools/MatTomo/@ImodObject
ImportExportTools/MatTomo/@ImodObject/private
ImportExportTools/MatTomo/@MRCImage
ImportExportTools/MatTomo/@MRCImage/private
ImportExportTools/MatTomo/Utils
ImportExportTools/MatTomo/Visualization
ImportExportTools/Omero
ImportExportTools/export_fig
ImportExportTools/nrrd
Plugins/File Processing/ImageConverter
Plugins/IntensityAnalysis/TripleAreaIntensity
Plugins/MyPlugins/mibAppDesignPlugin
Plugins/MyPlugins/mibPlugin
Plugins/MyPlugins/mibPluginWithoutGUI
Plugins/MyPlugins/myPluginName
Plugins/Organelle Analysis/Granularity
Plugins/Organelle Analysis/MCcalc
Plugins/Organelle Analysis/MCcalc/v1
Plugins/Organelle Analysis/SurfaceArea3D
Plugins/Organelle Analysis/ThreshAnalysisForObjects
Plugins/Plasmodesmata/CellWallThickness
Plugins/Plasmodesmata/SpacialControlPoints
Plugins/Tutorials/GuiTutorial
Tools
Tools/CellMigration
Tools/FastMarching
Tools/FastMarching/functions
Tools/FastMarching/shortestpath
Tools/Frangi
Tools/HistThresh
Tools/RandomForest/MembraneDetection
Tools/RandomForest/RF_Class_C
Tools/RandomForest/RF_Reg_C
Tools/RegionGrowing
Tools/Supervoxels
Tools/matGeom/geom2d
Tools/matGeom/geom3d
Tools/mibDeepSupport
Tools/prettify_MATLAB_html/publish overload
jars/xlwrite
techdoc
techdoc/prettify documentation
techdoc/publish overload
Plugins/IntensityAnalysis/TripleAreaIntensity
Plugins/Organelle Analysis/SurfaceArea3D
techdoc
techdoc/prettify documentation
Versions that use the GitHub default branch cannot be downloaded
Version | Published | Release Notes | |
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2.8020 | bug fixes:
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2.8002 | bug fix |
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2.8001 | updated description |
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2.80 | The update includes multiple improvements especially in training and segmentation of 2D convolutional neural networks with DeepMIB.
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2.70 | - deep learning with DeepMIB to train deep convolutional networks for image segmentation
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2.60 | Batch processing mode demo
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2.1.0.0 | added a demo image |
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