Microscopy Image Browser 2 (MIB2)

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:

http://mib.helsinki.fi/acknowledgements.html

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 , 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

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 (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)

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 (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)

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 projections and focus stacking
• Morphological operations

Visualization

• 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