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Microscopy Image Browser (MIB)
version 1.302.0.0 (41.1 MB) by
Ilya Belevich
MIB is a package for segmentation of multi-dimensional (2D-4D) microscopy datasets
912 Downloads
Updated 09 Feb 2019
From GitHub
Version History
Versions that use the GitHub default branch cannot be downloaded
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1.302.0.0 | 1.302 Improved and simplified the segmentation panel
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1.23.0.0 | new image alignment; IMOD enhanced compatibility, improvements and bug fixes
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1.2.0.0 | Version 1.20 20.06.2016 (volume rendering/new installer) |
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1.1.0.0 | updated description |
PLEASE NOTE!
This is an older version tree of MIB, the newer version for Matlab R2014b and newer available from here
http://se.mathworks.com/matlabcentral/fileexchange/63402-microscopy-image-browser-2--mib2-
With MIB you can analyse, segment and visualize various multidimensional datasets from both light and electron microscopy.
See more further details and tutorials on MIB website: http://mib.helsinki.fi/index.html
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
Cite As
Ilya Belevich (2021). Microscopy Image Browser (MIB) (https://github.com/Ajaxels/MIB), GitHub. Retrieved .
Requires
Tested with Matlab R2011a - R2016a
Some additional optional requirements are mentioned here:
http://mib.helsinki.fi/downloads_systemreq.html
http://se.mathworks.com/matlabcentral/fileexchange/help_tags
MATLAB Release Compatibility
Created with
R2011a
Compatible with any release
Platform Compatibility
Windows macOS LinuxCategories
Acknowledgements
Inspired by: view3d.m, Local Normalization, extrema.m, extrema2.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, Image Edge Enhancing Coherence Filter Toolbox, Highly portable JSON-input parser, Jann5s/measuretool, Render RGB text over RGB or Grayscale Image, improved xlswrite.m, xml2struct, struct2xml, IMCLIPBOARD, Hardware accelerated 3D viewer for MATLAB, mdrohmann/mtocpp, NRRD Format File Reader, drifty_shifty_deluxe.m, regionprops3
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Classes/@Labels
Classes/@Measure
Classes/@imageData
- addColorChannel
- clearContents
- clearMask
- clearSelection
- convertDataToMouseCoordinates
- convertImage
- convertModel
- convertMouseToDataCoordinates
- copyColorChannel
- createModel
- cropDataset
- deleteColorChannel
- deleteSlice
- generateModelColors
- getBoundingBox
- getCoordinatesOfShownImage
- getCurrentSlice
- getCurrentSliceNumber
- getCurrentTimePoint
- getData2D
- getData3D
- getData4D
- getDataset
- getDatasetDimensions
- getDatasetSizeInBytes
- getFullSlice
- getMaterialNames
- getRGBimage
- getRoiCrop
- getRoiCropSlice
- getSlice
- getSliceToShow
- imageData
- insertEmptyColorChannel
- insertSlice
- invertColorChannel
- mark2selection
- moveMaskToSelectionDataset
- moveModelToMaskDataset
- moveModelToSelectionDataset
- moveSelectionToMaskDataset
- moveSelectionToModelDataset
- moveView
- plotImage
- replaceDataset
- replaceImageColor
- resizeImage
- rotateColorChannel
- setCurrentSlice
- setData2D
- setData3D
- setData4D
- setDataset
- setFullSlice
- setMaterialNames
- setRoiCrop
- setRoiCropSlice
- setSlice
- setSliceToShow
- swapColorChannels
- transpose
- updateAxesLimits
- updateBoundingBox
- updateDisplayParameters
- updateImgInfo
- updateParameters
Classes/@imageUndo
Classes/@roiRegion
GuiTools
- backgroundRemovalGUI_Callback
- backgroundStrelSmoothingChk_Callback
- brushSuperpixelsCheck
- bufferToggles_cb
- changelayerEdit_Callback
- changelayerSlider_Callback
- changeTimeEdit_Callback
- changeTimeSlider_Callback
- channelMixerTable_CellSelectionCallback
- createModelBtn_Callback
- editbox_Callback
- filesListboxContext_cb
- getClickPoint
- ib_aboutDlg
- ib_addIcons
- ib_channelMixerTable_Callback
- ib_checkUpdate
- ib_cropGui
- ib_datasetInfoGui
- ib_do_backup
- ib_do_undo
- ib_getDataset
- ib_getSlice
- ib_getStack
- ib_labelsGui
- ib_moveLayers
- ib_resampleGui
- ib_setDataset
- ib_setSlice
- ib_setStack
- ib_updateCursor
- ib_updateFontSize
- imAdjustBtn_Callback
- imAdjustments
- imageFilterDoitBtn_Callback
- imageFilterPopup_Callback
- imfiltPar1Edit_Callback
- imfiltPar2Edit_Callback
- im_browser_brush_scrollWheelFcn
- im_browser_CloseRequestFcn
- im_browser_filesListbox_Callback
- im_browser_panAxesFcn
- im_browser_PanelShiftBtnUpFcn
- im_browser_ResizeFcn
- im_browser_scrollWheelFcn
- im_browser_WindowBrushMotionFcn
- im_browser_WindowButtonDownFcn
- im_browser_WindowKeyPressFcn
- im_browser_WindowKeyPressFcn_BrushSuperpixel
- im_browser_WindowKeyReleaseFcn
- im_browser_winMouseMotionFcn
- loadModelBtn_Callback
- localNormSigmaSlider_Callback
- logList
- magicwandMethodPopup_Callback
- maskShowCheck_Callback
- menuDatasetAlignDatasets
- menuDatasetBoundingBox
- menuDatasetCrop
- menuDatasetResample
- menuDatasetSlice
- menuDatasetTransform
- menuFileChoppedImage
- menuFileExportImage
- menuFileImportImage
- menuFileMakeMovie
- menuFileOmeroImport
- menuFilePreferences
- menuFileSaveImageAs
- menuFileSnapshot
- menuImageColorCh
- menuImageContrast
- menuImageConvert
- menuImageIntensity
- menuImageMode
- menuImageProfileArbitrary_Callback
- menuImageProfileLine_Callback
- menuMaskImport
- menuMaskInvert
- menuMaskLoad
- menuMaskSaveAs
- menuModelFillMembrane
- menuModelsExport
- menuModelsImport
- menuModelsSaveAs
- menuSelectionBuffer
- menuSelectionBufferCopy_Callback
- menuSelectionInterpolate
- menuSelectionInvert
- menuSelectionToMaskBorder
- menuToolsMeasure
- mibGUI_WindowButtonUpFcn
- mib_BoundingBoxDlg
- mib_calibrateScaleBar
- mib_contrastContext_cb
- mib_inputdlg
- mib_keyShortcutsDlg
- mib_measureTool
- mib_rescaleWidgets
- modelShowCheck_Callback
- model_cm_Callback
- pathEdit_Callback
- pixInfo_cb
- preferencesDlg
- recentDirsPopup_Callback
- redrawChannelMixerTable
- removeMaterialBtn_Callback
- roiAddBtn_Callback
- roiList_cm_Callback
- roiLoadBtn_Callback
- roiRemoveBtn_Callback
- roiRoiToSelectionBtn_Callback
- roiSaveBtn_Callback
- roiShowCheck_Callback
- roiTypePopup_Callback
- saveModelToolbar_ClickedCallback
- scrollbarClick_Callback
- segmSelectedOnlyCheck_Callback
- segmTable_CellSelectionCallback
- selectionButton_Callback
- selectionClearBtn_Callback
- selectionDilateBtn_Callback
- selectionErBtn_Callback
- selectionFillBtn_Callback
- seltypePopup_Callback
- smoothImage_Callback
- toolbarInterpolation
- toolbarPlaneToggle
- toolbarResizingMethod
- toolbar_zoomBtn
- unFocus
- updateGuiWidgets
- updateMIB
- updateSegmentationTable
- update_drives
- update_filelist
- zoomEdit_Callback
GuiTools/volren
- affine_transform_2d_double
- getRGBvolume
- image_interpolation
- makeViewMatrix
- render
- volrenToolbarSwitch_ClickedCallback
- volren_scrollWheelFcn
- volren_WindowButtonDownFcn
- volren_WindowButtonUpFcn
- volren_WindowInteractMotionFcn
- volren_winMouseMotionFcn
ImageFilters
- anisodiff
- do_andiff_filtering
- do_andiff_filtering_backup
- do_diplib_andiff_filtering
- getFrangiMask
- getMorphMask
- getStrelMask
- get_black_white_filter
- ib_anisotropicDiffusion
- ib_autoBrightness
- ib_contrastCLAHE
- ib_contrastNormalizationMemoryOptimized
- ib_dilateSelection
- ib_doImageFiltering
- ib_erodeSelection
- ib_fillMembranes
- ib_imageMorphOpsGui
- ib_linearContrast
- ib_MorphOpsGui
- ib_removeBackground
- ib_smoothImage
- ib_watershedGui
- ManGridBW
ImageFilters/Coherence_filter
ImageFilters/Coherence_filter/functions
ImageFilters/Coherence_filter/functions2D
- CoherenceFilterStep2D.m
- ConstructDiffusionTensor2D
- diffusion_scheme_2D_implicit
- diffusion_scheme_2D_non_negativity
- diffusion_scheme_2D_novel
- diffusion_scheme_2D_rotation_invariant
- diffusion_scheme_2D_standard
- EigenVectors2D
- hessian
- StructureTensor2D
- ut_gauss
ImageFilters/Coherence_filter/functions3D
- CoherenceFilterStep3D.m
- diffusion_scheme_3D_implicit
- diffusion_scheme_3D_non_negativity
- diffusion_scheme_3D_novel
- diffusion_scheme_3D_novel_getUpdate
- diffusion_scheme_3D_rotation_invariant
- diffusion_scheme_3D_standard
- EigenVectors3D
- StructureTensor2DiffusionTensor3D
- StructureTensor3D
ImageFilters/Coherence_filter/optimization
- error_diffusion_scheme_2D
- error_diffusion_scheme_3D
- fitgaussian
- fminlbfgs
- optimize_scheme_2D.m
- optimize_scheme_3D.m
ImageFilters/FastMarching
ImageFilters/FastMarching/functions
ImageFilters/FastMarching/shortestpath
ImageFilters/Frangi
ImageFilters/RandomForest
ImageFilters/RandomForest/MembraneDetection
- centeredRotate
- filterImageWithMembraneTemplateRotated
- filterSmallRegions
- gradientImg
- imsmooth
- makeColorOverlay
- membraneFeatures
- norm01
- normxcorr2_mex
- script_for_grayscale_distribution.m
- shiftDown
- shiftLeft
- shiftRight
- shiftUp
- skeletonize
- skript_applyClassifier_to_all_images.m
- skript_extractMembraneFeatures_for_allImages.m
- skript_trainClassifier_for_membraneDetection.m
- structureTensorImage2
- uint8Img
ImageFilters/RandomForest/RF_Class_C
- classRF_predict
- classRF_train
- compile_linux
- compile_windows
- test_ClassRF_extensively.m
- tutorial_ClassRF.m
ImageFilters/RandomForest/RF_Reg_C
ImageFilters/Supervoxels
ImportExportTools
- amiraLabels2bitmap
- amiraMesh2bitmap
- bitmap2amiraLabels
- bitmap2amiraMesh
- exportModelToImodModel
- getAmiraMeshHeader
- getImageMetadata
- getMRCfile
- getMRCheader
- ib_amiraImportGui
- ib_getImages
- ib_image2jpg
- ib_image2mrc
- ib_image2png
- ib_image2tiff
- ib_imwrite
- ib_loadImages
- ib_saveVideoGui
- ib_snapshotGui
- mib_chopDatasetGui
- mib_rechopDatasetGui
- parseStructToTree
- stlwrite
ImportExportTools/BioFormats
- bfCheckJavaMemory
- bfCheckJavaPath
- bfGetFileExtensions
- bfGetPlane
- bfGetReader
- bfInitLogging
- bfopen
- bfopen3
- bfOpen3DVolume
- bfsave
- bfUpgradeCheck
- createMinimalOMEXMLMetadata
- selectLociSeries
- wavelength2rgb
ImportExportTools/BioFormats/private
ImportExportTools/Fiji
- fijitest
- ib_exportToFiji
- ib_fijiSelectDataset
- ib_importFromFiji
- ib_renderModelFiji
- ib_renderVolumeWithFiji
- ib_runFijiMacro
- ib_startMiji
- ib_stopMiji
- Miji_deploy
- Miji_wrapper
ImportExportTools/HDF5
- getXMLheader
- image2hdf5
- loadBigDataViewerFormat
- mib_saveHDF5Dlg
- p_json
- readBigDataViewerFormat
- saveBigDataViewerFormat
- saveXMLheader
- selectHDFSeries
- struct2xml
- xml2struct
ImportExportTools/Imaris
- ib_getImarisDataset
- ib_getImarisDataset
- ib_renderModelImaris
- ib_setImarisDataset
- imaris_send_data_test.m
- SurfacesFromSegmentationImage
ImportExportTools/Imaris/@IceImarisConnector
- autocast
- closeImaris
- createAndSetSpots
- createDataset
- display
- findImaris
- getAllSurpassChildren
- getDataSubVolume
- getDataSubVolumeRM
- getDataVolume
- getDataVolumeRM
- getExtends
- getImarisVersionAsInteger
- getMatlabDatatype
- getSizes
- getSurpassCameraRotationMatrix
- getSurpassSelection
- getVoxelSizes
- IceImarisConnector
- indexingStart
- info
- isAlive
- isOfType
- isSupportedPlatform
- mapPositionsUnitsToVoxels
- mapPositionsVoxelsToUnits
- mapRgbaScalarToVector
- mapRgbaVectorToScalar
- mib_setDataSubVolume
- mib_setDataSubVolumeRM
- setDataVolume
- setDataVolumeRM
- startImaris
- startImarisServer
- version
ImportExportTools/MatTomo/@ImodChunk
ImportExportTools/MatTomo/@ImodChunk/private
ImportExportTools/MatTomo/@ImodContour
ImportExportTools/MatTomo/@ImodContour/private
ImportExportTools/MatTomo/@ImodMesh
ImportExportTools/MatTomo/@ImodMesh/private
ImportExportTools/MatTomo/@ImodModel
- appendObject
- close
- draw
- findRange
- getDefaultColor
- getIsFlipped
- getMax
- getNObjects
- getObject
- getObjectType
- getPixelSize
- getPoints
- getXScale
- getYScale
- getZScale
- ImodModel
- open
- setFilename
- setMax
- setObject
- setObjectType
- setPixelSize
- setPoints
- setXScale
- setYScale
- setZScale
- showHeader
- sortPoints
- write
ImportExportTools/MatTomo/@ImodModel/private
ImportExportTools/MatTomo/@ImodObject
- appendContour
- freadObject
- freadObjectMat
- getColor
- getContour
- getDrawSize
- getNContours
- getPoints
- getType
- ImodObject
- setColor
- setContour
- setDrawSize
- setName
- setType
- showHeader
- write
ImportExportTools/MatTomo/@ImodObject/private
ImportExportTools/MatTomo/@MRCImage
- addLabel
- addSphere
- close
- display
- filterProjection
- getCellX
- getCellY
- getCellZ
- getDimensions
- getFID
- getFilename
- getForceWriteByteMode
- getHeader
- getImage
- getMinAndMaxDensity
- getModeString
- getNX
- getNXStart
- getNY
- getNYStart
- getNZ
- getNZStart
- getSlice
- getStatistics
- getVolume
- isVolumeLoaded
- loadVolume
- MRCImage
- normalize
- open
- putImage
- save
- setFilename
- setForceWriteByteMode
- setNZ
- setPixelSize
- setSubvolume
- setVolume
- showHeader
- writeEM
- writeVTK
- zero
ImportExportTools/MatTomo/@MRCImage/private
- default
- defaultIMODStamp
- emptyVolume
- getFileNBytes
- getModeBytes
- getReadBytesAsSigned
- getWriteBytesAsSigned
- openWritable
- readHeader
- setStatisticsFromVolume
- setVolumeAndHeaderFromVolume
- writeHeader
ImportExportTools/MatTomo/Utils
ImportExportTools/MatTomo/Visualization
ImportExportTools/Omero
ImportExportTools/export_fig
ImportExportTools/nrrd
Misc_func
- bwdistsc
- bwdistsc1
- correlationAnalysis_script
- extrema
- extrema2
- findjobj
- findjobj
- imRAG
- imRichRAG
- my_ginput
- removeDotsFromFilePath
- rendertext
- view3d
- xlswrite2
Misc_func/imclipboard
Plugins/Demos/generateStereologyGrid
Plugins/Demos/ib_tubesVsSheets
Plugins/IntensityAnalysis/NucleusVsCytoplasm
Plugins/IntensityAnalysis/TripleAreaIntensity
Plugins/Tutorials/guiTutorial
Plugins/Tutorials/otsuThresholding
Tools
- calc_correlation.m
- generate_grid_block_size
- ib_addText2Img
- ib_calcCorrelation
- ib_calculatePixSizes
- ib_calculateResolution
- ib_connectPoints
- ib_connect_points
- ib_flipDataset
- ib_interpolateLines
- ib_interpolateShapes
- ib_invertImage
- ib_maskGenerator
- ib_renderModel
- ib_rotateDataset
- ib_segmentation_3dBall
- ib_segmentation_Annotation
- ib_segmentation_Brush
- ib_segmentation_Lasso
- ib_segmentation_MagicWand
- ib_segmentation_MembraneClickTraker
- ib_segmentation_ObjectPicker
- ib_segmentation_RegionGrowing
- ib_segmentation_SmartWatershed
- ib_segmentation_Spot
- ib_segmentBlackWhiteThreshold
- ib_sizeExclusionFilter
- ib_transposeDataset
- ib_updatePixSizeAndResolution
- mark2selection
- mib_compile_c_files.m
- mib_resize3d
- mib_stereologyGui
Tools/Align
Tools/AreaAnalysis
Tools/RegionGrowing
techdoc
Plugins/Demos/ib_tubesVsSheets
Plugins/IntensityAnalysis/NucleusVsCytoplasm
Plugins/IntensityAnalysis/TripleAreaIntensity
techdoc
- Acknowledgements
- Alignment and Drift Correction
- Background Removal Panel
- Chopped images...
- Classifier of superpixels / supervoxels
- Correlation Analysis Panel
- Data layers of Microscopy Image Browser (Image, Model, Mask, Selection)
- Dataset Menu
- Directory Contents Panel
- Edge Enhancing Coherence Filter in the Image Filters Panel
- Fiji Connect Panel
- File Menu
- Help Menu
- Image Filters Panel
- Image Menu
- Image View Panel
- Key & mouse shortcuts
- Make a snapshot to a file or to clipboard.
- Make movie
- Mask Generators panel
- Mask Menu
- Microscopy Image Browser
- Microscopy Image Browser
- Microscopy Image Browser Features
- Microscopy Image Browser Getting Started
- Microscopy Image Browser Installation
- Microscopy Image Browser License
- Microscopy Image Browser Measure Tool
- Microscopy Image Browser Menus
- Microscopy Image Browser Panels
- Microscopy Image Browser Preferences
- Microscopy Image Browser Release Notes
- Microscopy Image Browser System Requirements
- Microscopy Image Browser Toolbar
- Microscopy Image Browser Troubleshooting
- Microscopy Image Browser Tutorials
- Microscopy Image Browser Watershed/Graphcut segmentation
- Model Menu
- Path Panel
- Plugins Menu
- Random Forest Classifier
- ROI Panel
- Segmentation Panel
- Segmentation Tools
- Selection Menu
- Selection Panel
- Statistics for Mask or Model objects
- The Adjust display window
- The View Settings Panel
- Tools Menu
To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.
