Microscopy Image Browser 2 (MIB2)
version 2.8020 (67.4 MB) by
Ilya Belevich
MIB2 is an update package for segmentation of multi-dimensional (2D-4D) microscopy datasets
With MIB2 you can analyse, segment and visualize various multidimensional datasets from both light and electron microscopy. MIB2 is completely rewritten to follow MVC architecture and brings additional stability among many new features.
See more further details and tutorials on MIB website:
http://mib.helsinki.fi
I would like to acknowledge Matlab File Exchange user community and especially the authors whose functions were utilized during development of the program:
The MIB version 1 is available from here
http://se.mathworks.com/matlabcentral/fileexchange/56481-microscopy-image-browser--mib-
and recommended for Matlab version: R2011a - 2014a
List of all features with video tutorials is available from
http://mib.helsinki.fi/features_all.html
Features:
- 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
Data import/export
- Direct import/export with Matlab, Fiji, Imarisand system clipboard
- Direct import from Omero serverand 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
Quantification and Statistics
- 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)
Measurements
- Angles
- Caliper
- Circle, radius
- Freehand distance and intensity profile
- Linear distance and intensity profile
- Polyline distance and intensity profile
- Stereology
- Wound healing assay
Segmentation tools
- 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 (分支点,对角填补,结束点,骨架, 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)
Segmentation tools
- 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 (分支点,对角填补,结束点,骨架, 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)
Image Processing
- 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 projectionsand focus stacking
- Morphological operations
Visualization
- Orthoslices (XY, ZX, ZY planes)
- Volume Rendering (hardware)
- Volume Rendering (software)
- Models with Matlab isosurfaces
- 模型和卷with Fiji 3D viewer
- 模型和卷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 (2021).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
Created with R2021a
Compatible with R2014b and later releases
Platform Compatibility
Windows macOS LinuxCategories
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,NRRD Format File Reader,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/@mibDeepController/backup
Classes/@mibDragNDropControl
Classes/@mibExternalDirsController
Classes/@mibGraphcutController
Classes/@mibHistThresController
Classes/@mibImage
Classes/@mibImageAdjController
Classes/@mibImageArithmeticController
Classes/@mibImageFiltersController
类/ @mibImageMorphOpsController
Classes/@mibImageSelectFrameController
类/ @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
类/ @mibRandomDatasetController
Classes/@mibRandomRestoreDatasetController
Classes/@mibRechopDatasetController
Classes/@mibResampleController
Classes/@mibRoiRegion
Classes/@mibSnapshotController
Classes/@mibStatisticsController
Classes/@mibStereologyController
Classes/@mibSupervoxelClassifierController
Classes/@mibTipsController
Classes/@mibUpdateCheckController
Classes/@mibView
Classes/@mibVolRenController
Classes/@mibWatershedController
Classes/@mibWoundHealingAssayController
Classes/@volrenAnimationController
Development/mibPluginGUI_ver1
Development/mibPluginGUI_ver2_Batch_compatible
Development/mibPluginGUI_ver3_appDesigner
Development/mibPlugin_withoutGUI
GuiTools
GuiTools/volren
不重要xportTools
不重要xportTools/Amira
不重要xportTools/BioFormats
不重要xportTools/BioFormats/private
不重要xportTools/Fiji
不重要xportTools/HDF5
不重要xportTools/IMOD
不重要xportTools/IMOD/@ImodChunk
不重要xportTools/IMOD/@ImodChunk/private
不重要xportTools/IMOD/@ImodContour
不重要xportTools/IMOD/@ImodContour/private
不重要xportTools/IMOD/@ImodMesh
不重要xportTools/IMOD/@ImodMesh/private
不重要xportTools/IMOD/@ImodModel
不重要xportTools/IMOD/@ImodModel/private
不重要xportTools/IMOD/@ImodObject
不重要xportTools/IMOD/@ImodObject/private
不重要xportTools/IMOD/@MRCImage
不重要xportTools/IMOD/@MRCImage/private
不重要xportTools/IMOD/Visualization
不重要xportTools/Imaris
不重要xportTools/Imaris/@IceImarisConnector
不重要xportTools/MatTomo/@ImodChunk
不重要xportTools/MatTomo/@ImodChunk/private
不重要xportTools/MatTomo/@ImodContour
不重要xportTools/MatTomo/@ImodContour/private
不重要xportTools/MatTomo/@ImodMesh
不重要xportTools/MatTomo/@ImodMesh/private
不重要xportTools/MatTomo/@ImodModel
不重要xportTools/MatTomo/@ImodModel/private
不重要xportTools/MatTomo/@ImodObject
不重要xportTools/MatTomo/@ImodObject/private
不重要xportTools/MatTomo/@MRCImage
不重要xportTools/MatTomo/@MRCImage/private
不重要xportTools/MatTomo/Utils
不重要xportTools/MatTomo/Visualization
不重要xportTools/Omero
不重要xportTools/export_fig
不重要xportTools/nrrd
Plugins/File Processing/ImageConverter
Plugins/IntensityAnalysis/TripleAreaIntensity
Plugins/MyPlugins/mibAppDesignPlugin
Plugins/MyPlugins/mibPlugin
Plugins/MyPlugins/mibPluginWithoutGUI
Plugins/MyPlugins/myPluginName
Plugins/Organelle Analysis/MCcalc
Plugins/Organelle Analysis/SurfaceArea3D
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
工具/ RandomForest / RF_Class_C
Tools/RandomForest/RF_Reg_C
Tools/RegionGrowing
Tools/Supervoxels
Tools/matGeom/geom2d
Tools/matGeom/geom3d
jars/xlwrite
techdoc
Plugins/IntensityAnalysis/TripleAreaIntensity
Plugins/Organelle Analysis/SurfaceArea3D
techdoc
To view or report issues in this GitHub add-on, visit theGitHub Repository.
To view or report issues in this GitHub add-on, visit theGitHub Repository.
