 |
Microscopy Image Browser 2.91
MIB
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Microscopy Image Browser 2.91
MIB
|
| ► Classes | |
| ► @Labels | |
| Labels.m | |
| ► @Lines3D | |
| Lines3D.m | |
| ► @mibAboutController | |
| mibAboutController.m | |
| ► @mibAlignmentController | |
| alignDriftCorrectionHDD.m | |
| AlignMedianSmoothTemplate.m | |
| automaticFeatureBasedAlignmentHDD.m | |
| automaticFeatureBasedAlignmentHDDv2.m | |
| AutomaticFeatureBasedAlignmentV2.m | |
| mibAlignmentController.m | |
| ► @mibAnnotationsController | |
| mibAnnotationsController.m | |
| ► @mibBatchController | |
| mibBatchController.m | |
| obtainDirectoryForAction.m | |
| updateWidgets.m | |
| ► @mibBoundingBoxController | |
| mibBoundingBoxController.m | |
| ► @mibChildView | |
| mibChildView.m | |
| ► @mibChopDatasetController | |
| mibChopDatasetController.m | |
| ► @mibController | |
| devTest_ClickedCallback.m | |
| exitProgram.m | |
| findChildId.m | |
| generateDefaultPreferences.m | |
| getDefaultParameters.m | |
| getMeta.m | |
| imageRedraw.m | |
| menuDatasetParameters_Callback.m | |
| menuDatasetScalebar_Callback.m | |
| menuDatasetSlice_Callback.m | |
| menuDatasetTrasform_Callback.m | |
| menuFileChoppedImage_Callback.m | |
| menuFileExamples_Callback.m | |
| menuFileExportImage_Callback.m | |
| menuFileImportImage_Callback.m | |
| menuFilePreference_Callback.m | |
| menuFileRender_Callback.m | |
| menuFileSaveImageAs_Callback.m | |
| menuImageColorCh_Callback.m | |
| menuImageContrast_Callback.m | |
| menuImageIntensity_Callback.m | |
| menuImageInvert_Callback.m | |
| menuImageMode_Callback.m | |
| menuImageToolsContentAware_Callback.m | |
| menuImageToolsProjection_Callback.m | |
| menuMaskExport_Callback.m | |
| menuMaskImageReplace_Callback.m | |
| menuMaskImport_Callback.m | |
| menuMaskInvert_Callback.m | |
| menuMaskLoad_Callback.m | |
| menuMaskSaveAs_Callback.m | |
| menuModelAnn_Callback.m | |
| menuModelsExport_Callback.m | |
| menuModelsImport_Callback.m | |
| menuModelsRender_Callback.m | |
| menuModelsSaveAs_Callback.m | |
| menuSelectionBuffer_Callback.m | |
| menuSelectionInterpolate.m | |
| menuSelectionToMaskBorder_Callback.m | |
| menuSmooth_Callback.m | |
| menuToolsMeasure_Callback.m | |
| mibAddMaterialBtn_Callback.m | |
| mibAnisotropicDiffusion.m | |
| mibAnnMarkerEdit_Callback.m | |
| mibAutoBrightnessBtn_Callback.m | |
| mibBioformatsCheck_Callback.m | |
| mibBrushPanelInterpolationSettingsBtn_Callback.m | |
| mibBrushSuperpixelsEdit_Callback.m | |
| mibBrushSuperpixelsWatershedCheck_Callback.m | |
| mibBufferToggle_Callback.m | |
| mibBufferToggleContext_Callback.m | |
| mibChangeLayerEdit_Callback.m | |
| mibChangeLayerSlider_Callback.m | |
| mibChangeTimeEdit_Callback.m | |
| mibChangeTimeSlider_Callback.m | |
| mibChannelMixerTable_Callback.m | |
| mibChannelMixerTable_CellEditCallback.m | |
| mibChannelMixerTable_CellSelectionCallback.m | |
| mibColChannelCombo_Callback.m | |
| mibController.m | |
| mibCreateModelBtn_Callback.m | |
| mibDoUndo.m | |
| mibDragAndDropFiles.m | |
| mibDragAndDropModelFiles.m | |
| mibEraserEdit_Callback.m | |
| mibFijiExport.m | |
| mibFijiImport.m | |
| mibFijiRunMacro.m | |
| mibFileFilterPopup_cm.m | |
| mibFilesListbox_Callback.m | |
| mibFilesListbox_cm_Callback.m | |
| mibFindMaterialUnderCursor.m | |
| mibGUI_Brush_scrollWheelFcn.m | |
| mibGUI_panAxesFcn.m | |
| mibGUI_PanelShiftBtnUpFcn.m | |
| mibGUI_ScrollWheelFcn.m | |
| mibGUI_SizeChangedFcn.m | |
| mibGUI_WindowBrushMotionFcn.m | |
| mibGUI_WindowButtonDownFcn.m | |
| mibGUI_WindowButtonUpDragAndDropFcn.m | |
| mibGUI_WindowButtonUpFcn.m | |
| mibGUI_WindowDragAndDropMotionFcn.m | |
| mibGUI_WindowKeyPressFcn.m | |
| mibGUI_WindowKeyPressFcn_BrushSuperpixel.m | |
| mibGUI_WindowKeyReleaseFcn.m | |
| mibGUI_WinMouseMotionFcn.m | |
| mibImageFilterDoitBtn_Callback.m | |
| mibLoadModelBtn_Callback.m | |
| mibLutCheckbox_Callback.m | |
| mibMaskedAreaCheck_Callback.m | |
| mibMaskGenerator.m | |
| mibMaskRecalcStatsBtn_Callback.m | |
| mibMaskShowCheck_Callback.m | |
| mibModelPropertyUpdate.m | |
| mibModelShowCheck_Callback.m | |
| mibPixelInfo_Callback.m | |
| mibRecolorLabels.m | |
| mibRemoveMaterialBtn_Callback.m | |
| mibRoiAddBtn_Callback.m | |
| mibRoiList_cm_Callback.m | |
| mibRoiLoadBtn_Callback.m | |
| mibRoiOptionsBtn_Callback.m | |
| mibRoiRemoveBtn_Callback.m | |
| mibRoiSaveBtn_Callback.m | |
| mibRoiShowCheck_Callback.m | |
| mibRoiToSelectionBtn_Callback.m | |
| mibSegmAnnDeleteAllBtn_Callback.m | |
| mibSegmentation3dBall.m | |
| mibSegmentationAnnotation.m | |
| mibSegmentationBlackWhiteThreshold.m | |
| mibSegmentationBrush.m | |
| mibSegmentationDragAndDrop.m | |
| mibSegmentationLasso.m | |
| mibSegmentationLassoManual.m | |
| mibSegmentationLines3D.m | |
| mibSegmentationMagicWand.m | |
| mibSegmentationMembraneClickTraker.m | |
| mibSegmentationObjectPicker.m | |
| mibSegmentationPanelCheckboxes.m | |
| mibSegmentationRegionGrowing.m | |
| mibSegmentationSAM.m | |
| mibSegmentationSAM2.m | |
| mibSegmentationSAM_requirements.m | |
| mibSegmentationSpot.m | |
| mibSegmentationTable_CellSelectionCallback.m | |
| mibSegmentationTable_cm_Callback.m | |
| mibSegmentationToolPopup_Callback.m | |
| mibSegmFavToolCheck_Callback.m | |
| mibSegmSAMPanel_Callbacks.m | |
| mibSegmSelectedOnlyCheck_Callback.m | |
| mibSelectionButton_Callback.m | |
| mibSelectionClearBtn_Callback.m | |
| mibSelectionDilateBtn_Callback.m | |
| mibSelectionErodeBtn_Callback.m | |
| mibSelectionFillBtn_Callback.m | |
| mibSelectionPanelCheckboxes.m | |
| mibShowMilestoneDialog.m | |
| mibToolbar_ZoomBtn_ClickedCallback.m | |
| mibToolbarPlaneToggle.m | |
| mibUpdatePresetFromSegmentationSettings.m | |
| mibUpdateSegmentationSettingsFromPreset.m | |
| mibViewSettingsPanelCheckboxes.m | |
| mibZoomEdit_Callback.m | |
| plotImage.m | |
| redrawMibChannelMixerTable.m | |
| setMeta.m | |
| startController.m | |
| startPlugin.m | |
| toolbarBlockModeSwitch_ClickedCallback.m | |
| toolbarCenterPointShow_ClickedCallback.m | |
| toolbarInterpolation_ClickedCallback.m | |
| toolbarRedo_ClickedCallback.m | |
| toolbarResizingMethod_ClickedCallback.m | |
| toolbarUndo_ClickedCallback.m | |
| toolbarVirtualMode_ClickedCallback.m | |
| updateAxesLimits.m | |
| updateFilelist.m | |
| updateGuiWidgets.m | |
| updateMyPath.m | |
| updateSegmentationTable.m | |
| updateShownId.m | |
| volren_scrollWheelFcn.m | |
| volren_WindowButtonDownFcn.m | |
| volren_WindowButtonUpFcn.m | |
| volren_WindowInteractMotionFcn.m | |
| volren_winMouseMotionFcn.m | |
| volrenToolbarSwitch_ClickedCallback.m | |
| ► @mibCropController | |
| mibCropController.m | |
| ► @mibCropObjectsController | |
| mibCropObjectsController.m | |
| ► @mibDatasetInfoController | |
| mibDatasetInfoController.m | |
| ► @mibDebrisRemovalController | |
| mibDebrisRemovalController.m | |
| ► @mibDeepController | |
| createNetwork.m | |
| findChildId.m | |
| generate3DDeepLabV3Network.m | |
| generateDeepLabV3Network.m | |
| generateUnet2DwithEncoder.m | |
| mibDeepController.m | |
| preprareTrainingOptionsInstances.m | |
| processImagesForInstanceSegmentation.m | |
| startController.m | |
| startTraining.m | |
| startTrainingInstances.m | |
| ► @mibDragNDropControl | |
| mibDragNDropControl.m | |
| ► @mibExternalDirsController | |
| mibExternalDirsController.m | |
| ► @mibGraphcutController | |
| mibGraphcut_CalcSupervoxels.m | |
| mibGraphcutController.m | |
| test_imRichRAG_2d.m | |
| ► @mibHistThresController | |
| mibHistThresController.m | |
| ► @mibImage | |
| addColorChannel.m | |
| addFrameToImage.m | |
| addStack.m | |
| clearContents.m | |
| clearMask.m | |
| clearSelection.m | |
| closeVirtualDataset.m | |
| convertImage.m | |
| convertModel.m | |
| convertPixelIdxListCrop2Full.m | |
| convertPixelsToUnits.m | |
| convertUnitsToPixels.m | |
| copyColorChannel.m | |
| copySlice.m | |
| createModel.m | |
| cropDataset.m | |
| deleteColorChannel.m | |
| deleteSlice.m | |
| generateModelColors.m | |
| getBoundingBox.m | |
| getCoordinatesOfShownImage.m | |
| getCurrentSliceNumber.m | |
| getCurrentTimePoint.m | |
| getData.m | |
| getDatasetDimensions.m | |
| getDatasetSizeInBytes.m | |
| getDataVirt.m | |
| getImAdjustStretchCoef.m | |
| getPixelIdxList.m | |
| getROIBoundingBox.m | |
| getSelectedMaterialIndex.m | |
| getSliceLabels.m | |
| insertEmptyColorChannel.m | |
| insertSlice.m | |
| invertColorChannel.m | |
| materialsInsert.m | |
| materialsRemove.m | |
| materialsRename.m | |
| materialsReorder.m | |
| materialsSwap.m | |
| materialsSwapColors.m | |
| mibImage.m | |
| modelExportToMatlab.m | |
| moveMaskToModelDataset.m | |
| moveMaskToSelectionDataset.m | |
| moveModelToMaskDataset.m | |
| moveModelToSelectionDataset.m | |
| moveSelectionToMaskDataset.m | |
| moveSelectionToModelDataset.m | |
| moveView.m | |
| replaceImageColor.m | |
| resliceDataset.m | |
| rotateColorChannel.m | |
| saveImageAsDialog.m | |
| saveMask.m | |
| saveModel.m | |
| setData.m | |
| setPixelIdxList.m | |
| shiftColorChannel.m | |
| swapColorChannels.m | |
| swapSlices.m | |
| switchVirtualStackingMode.m | |
| transpose.m | |
| updateBoundingBox.m | |
| updateDisplayParameters.m | |
| updateImgInfo.m | |
| updatePixSizeResolution.m | |
| updateServiceMetadata.m | |
| updateSlicesStructure.m | |
| ► @mibImageAdjController | |
| mibImageAdjController.m | |
| ► @mibImageArithmeticController | |
| mibImageArithmeticController.m | |
| ► @mibImageFiltersController | |
| Filter.m | |
| mibImageFiltersController.m | |
| ► @mibImageMorphOpsController | |
| mibImageMorphOpsController.m | |
| ► @mibImageSelectFrameController | |
| mibImageSelectFrameController.m | |
| ► @mibImageUndo | |
| mibImageUndo.m | |
| ► @mibImportOmeroController | |
| mibImportOmeroController.m | |
| ► @mibKeyShortcutsController | |
| mibKeyShortcutsController.m | |
| ► @mibLines3DController | |
| mibLines3DController.m | |
| ► @mibLogListController | |
| mibLogListController.m | |
| ► @mibMakeMovieController | |
| mibMakeMovieController.m | |
| ► @mibMeasure | |
| mibMeasure.m | |
| ► @mibMeasureToolController | |
| mibMeasureToolController.m | |
| ► @mibMembraneDetectionController | |
| mibMembraneDetectionController.m | |
| ► @mibModel | |
| addFrame.m | |
| clearMask.m | |
| clearSelection.m | |
| colorChannelActions.m | |
| contentAwareFill.m | |
| contrastCLAHE.m | |
| contrastNormalization.m | |
| convertDataToMouseCoordinates.m | |
| convertModel.m | |
| convertMouseToDataCoordinates.m | |
| copySwapSlice.m | |
| createModel.m | |
| deleteSlice.m | |
| dilateImage.m | |
| erodeImage.m | |
| fillSelectionOrMask.m | |
| flipDataset.m | |
| getAxesLimits.m | |
| getData2D.m | |
| getData3D.m | |
| getData4D.m | |
| getImageMethod.m | |
| getImageProperty.m | |
| getMagFactor.m | |
| getPixSize.m | |
| getRGBimage.m | |
| getRGBvolume.m | |
| insertEmptySlice.m | |
| interpolateImage.m | |
| invertImage.m | |
| loadMask.m | |
| loadModel.m | |
| materialsActions.m | |
| materialsSwapColors.m | |
| mibDoBackup.m | |
| mibImageDeepCopy.m | |
| mibModel.m | |
| modelExport.m | |
| moveLayers.m | |
| renameMaterial.m | |
| resliceDataset.m | |
| rotateDataset.m | |
| saveImageAsDialog.m | |
| saveMask.m | |
| saveModel.m | |
| setAxesLimits.m | |
| setData2D.m | |
| setData3D.m | |
| setData4D.m | |
| setDefaultSegmentationColorPalette.m | |
| setImageProperty.m | |
| setMagFactor.m | |
| setPixSize.m | |
| smoothImage.m | |
| transposeDataset.m | |
| transposeZ2T.m | |
| ► @mibMorphOpsController | |
| mibMorphOpsController.m | |
| ► @mibObjSepController | |
| mibObjSepController.m | |
| ► @mibPreferencesAppController | |
| mibPreferencesAppController.m | |
| ► @mibPreferencesController | |
| mibPreferencesController.m | |
| ► @mibRandomDatasetController | |
| mibRandomDatasetController.m | |
| ► @mibRandomRestoreDatasetController | |
| mibRandomRestoreDatasetController.m | |
| ► @mibRechopDatasetController | |
| mibRechopDatasetController.m | |
| ► @mibResampleController | |
| mibResampleController.m | |
| ► @mibRoiRegion | |
| mibRoiRegion.m | |
| ► @mibSnapshotController | |
| mibSnapshotController.m | |
| ► @mibStatisticsController | |
| mibStatisticsController.m | |
| ► @mibStereologyController | |
| mibStereologyController.m | |
| ► @mibSupervoxelClassifierController | |
| mibSupervoxelClassifierController.m | |
| ► @mibTipsAppController | |
| mibTipsAppController.m | |
| ► @mibTipsController | |
| mibTipsController.m | |
| ► @mibUpdateCheckController | |
| mibUpdateCheckController.m | |
| ► @mibView | |
| editbox_Callback.m | |
| getClickPoint.m | |
| getRoiSwitch.m | |
| getVolrenModeSwitch.m | |
| mibView.m | |
| setVolrenModeSwitch.m | |
| updateCursor.m | |
| ► @mibVolRenAppController | |
| findChildId.m | |
| mibVolRenAppController.m | |
| startController.m | |
| ► @mibVolRenAppViewerController | |
| mibVolRenAppViewerController.m | |
| ► @mibVolRenController | |
| findChildId.m | |
| mibVolRenController.m | |
| startController.m | |
| ► @mibWatershedController | |
| mibWatershedController.m | |
| ► @mibWhiteBalanceController | |
| mibWhiteBalanceController.m | |
| ► @mibWoundHealingAssayController | |
| mibWoundHealingAssayController.m | |
| ► @PoolWaitbar | |
| PoolWaitbar.m | |
| ► @ToggleEventData | |
| ToggleEventData.m | |
| ► @volrenAnimationController | |
| volrenAnimationController.m | |
| dicePixelCustomClassificationLayer.m | |
| dicePixelCustomClassificationLayer_backup.m | |
| mibDeepActivationsController.m | |
| mibDeepAugmentSettingsController.m | |
| ► GuiTools | |
| ► volren | |
| affine_transform_2d_double.c | |
| affine_transform_2d_double.m | Affine transformation function (Rotation, Translation, Resize) This function transforms a volume with a 3x3 transformation matrix |
| image_interpolation.c | |
| image_interpolation.h | |
| image_interpolation.m | This function is used to transform an 2D image, in a backwards way with an transformation image |
| makeViewMatrix.m | Rotation, resize and translation variables |
| render.m | Function RENDER will volume render a image of a 3D volume, with transperancy, shading and ColorTable |
| mibAboutGUI.m | MIBABOUTGUI MATLAB code for mibAboutGUI.fig MIBABOUTGUI, by itself, creates a new MIBABOUTGUI or raises the existing singleton* |
| mibAddIcons.m | Add icons to the menus |
| mibAlignmentGUI.m | MIBALIGNMENTGUI M-file for mibalignmentgui.fig MIBALIGNMENTGUI by itself, creates a new MIBALIGNMENTGUI or raises the existing singleton* |
| mibAnnotationsGUI.m | MibAnnotationsGUI is a GUI tool to show list of labels |
| mibBatchGUI.m | MIBBATCHGUI MATLAB code for mibBatchGUI.fig MIBBATCHGUI, by itself, creates a new MIBBATCHGUI or raises the existing singleton* |
| mibBoundingBoxGUI.m | Custom input dialog |
| mibCalculatePixSizes.m | Recalculate pixel size (width, height) of the dataset to new units |
| mibCalculateResolution.m | Calculate image resolution in Inch as default for saving tifs |
| mibChopDatasetGUI.m | MIBCHOPDATASETGUI MATLAB code for mibChopDatasetGUI.fig MIBCHOPDATASETGUI, by itself, creates a new MIBCHOPDATASETGUI or raises the existing singleton* |
| mibCropGUI.m | MibCropGUI function is responsible for the crop of dataset |
| mibCropObjectsGUI.m | MibCropObjectsGUI MATLAB code for mibCropObjectsGUI.fig mibCropObjectsGUI, by itself, creates a new mibCropObjectsGUI or raises the existing singleton* |
| mibDatasetInfoGUI.m | Mibdatasetinfogui is a GUI window that shows parameters of the dataset |
| mibExternalDirsGUI.m | MIBEXTERNALDIRSGUI MATLAB code for mibExternalDirsGUI.fig MIBEXTERNALDIRSGUI, by itself, creates a new MIBEXTERNALDIRSGUI or raises the existing singleton* |
| mibGraphcutGUI.m | MibGraphcutGUI function is responsible for watershed operations |
| mibGUI.m | MIBGUI MATLAB code for mibGUI.fig MIBGUI, by itself, creates a new MIBGUI or raises the existing singleton* |
| mibHistThresGUI.m | MibHistThresGUI function is responsible for morphological operations done with images |
| mibImageAdjustmentGUI.m | MibImageAdjustmentGUI function allows to adjust contrast and gamma of the shown dataset |
| mibImageArithmeticGUI.m | MIBIMAGEARITHMETICGUI MATLAB code for mibImageArithmeticGUI.fig MIBIMAGEARITHMETICGUI, by itself, creates a new MIBIMAGEARITHMETICGUI or raises the existing singleton* |
| mibImageMorphOpsGUI.m | MibImageMorphOpsGUI function is responsible for morphological operations done with images |
| mibImageSelectFrameGUI.m | MibImageSelectFrameGUI function is responsible for morphological operations done with images |
| mibImportOmeroGUI.m | MibImportOmeroGUI function is responsible for a dialog to advanced opening images from OMERO servers |
| mibInputDlg.m | Custom input dialog |
| mibInputMultiDlg.m | Custom input dialog |
| mibKeyShortcutsGUI.m | MIBKEYSHORTCUTSGUI MATLAB code for mibKeyShortcutsGUI.fig MIBKEYSHORTCUTSGUI, by itself, creates a new MIBKEYSHORTCUTSGUI or raises the existing singleton* |
| mibLines3DGUI.m | MibLines3DGUI is a GUI tool to show list of labels |
| mibLogListGUI.m | MibLogListGUI function calls a window with Log list of actions that were performed with the dataset |
| mibMakeMovieGUI.m | MibMakeMovieGUI function is responsible for saving video files of the datasets |
| mibMaskStatsProps.m | MIBMASKSTATSPROPS MATLAB code for mibMaskStatsProps.fig MIBMASKSTATSPROPS, by itself, creates a new MIBMASKSTATSPROPS or raises the existing singleton* |
| mibMeasureToolGUI.m | MIBMEASURETOOLGUI MATLAB code for mibMeasureToolGUI.fig MIBMEASURETOOLGUI, by itself, creates a new MIBMEASURETOOLGUI or raises the existing singleton* |
| mibMembraneDetectionGUI.m | MibMembraneDetectionGUI function uses random forest classifier for segmentation. The function utilize Random Forest for Membrane Detection functions by Verena Kaynig see more http://www.kaynig.de/demos.html |
| mibMorphOpsGUI.m | MIBMORPHOPSGUI MATLAB code for mibMorphOpsGUI.fig MIBMORPHOPSGUI, by itself, creates a new MIBMORPHOPSGUI or raises the existing singleton* |
| mibObjSepGUI.m | MibObjSepGUI function is responsible for watershed operations |
| mibPreferencesGUI.m | Varargout = mibPreferencesGUI(varargin) mibPreferencesGUI a dialog responsible for setting preferences for im_browser.m |
| mibQuestDlg.m | Custom button input dialog |
| mibRandomDatasetGUI.m | MIBRANDOMDATASETGUI MATLAB code for mibRandomDatasetGUI.fig MIBRANDOMDATASETGUI, by itself, creates a new MIBRANDOMDATASETGUI or raises the existing singleton* |
| mibRandomRestoreDatasetGUI.m | MIBRANDOMRESTOREDATASETGUI MATLAB code for mibRandomRestoreDatasetGUI.fig MIBRANDOMRESTOREDATASETGUI, by itself, creates a new MIBRANDOMRESTOREDATASETGUI or raises the existing singleton* |
| mibRechopDatasetGUI.m | MIBRECHOPDATASETGUI MATLAB code for mibRechopDatasetGUI.fig MIBRECHOPDATASETGUI, by itself, creates a new MIBRECHOPDATASETGUI or raises the existing singleton* |
| mibResampleGUI.m | MibResampleGUI function is responsible for resampling of datasets |
| mibRescaleWidgets.m | Rescale widgets for different operating systems |
| mibSelectModelTypeDlg.m | Dialog to select type of the model |
| mibSnapshotGUI.m | MibSnapshotGUI function is responsible for making snapshots of the shown dataset |
| mibStatisticsGUI.m | Mibstatisticsgui is a GUI tool to generate statistics of 2D or 3D objects in the Model or Mask layers |
| mibStereologyGUI.m | MIBSTEREOLOGYGUI MATLAB code for mibstereologygui.fig MIBSTEREOLOGYGUI, by itself, creates a new MIBSTEREOLOGYGUI or raises the existing singleton* |
| mibSupervoxelClassifierGUI.m | MibSupervoxelClassifierGUI function uses random forest classifier for segmentation. The function utilize Random Forest for Membrane Detection functions by Verena Kaynig see more http://www.kaynig.de/demos.html |
| mibTipsGUI.m | MIBTIPSGUI MATLAB code for mibTipsGUI.fig MIBTIPSGUI, by itself, creates a new MIBTIPSGUI or raises the existing singleton* |
| mibUpdateCheckGUI.m | MIBUPDATECHECKGUI MATLAB code for mibUpdateCheckGUI.fig MIBUPDATECHECKGUI, by itself, creates a new MIBUPDATECHECKGUI or raises the existing singleton* |
| mibUpdateDrives.m | Updates list of available logical disk drives and updates handles.mibDrivePopup with that list |
| mibUpdateFontSize.m | Update font size for text widgets |
| mibUpdatePixSizeAndResolution.m | Calculate update resolution fields in the imageData.img_info(ImageDescription) or recalculate physical size of voxels |
| mibVolRenGUI.m | MibVolRenGUI function is responsible for morphological operations done with images |
| mibWatershedGUI.m | MibWatershedGUI function is responsible for watershed operations |
| moveWindowOutside.m | Determine the position of the dialog - on a side of the main figure if available, else, centered on the main figure Parameters: hObject: a handle of the window to be moved alignH: an optional string with the preferred horizontal alignment: left (default), right, center alignV: an optional string with the preferred vertical alignment: top (default), bottom, center |
| scrollbarClick_Callback.m | This is callback for the press of a mouse button above specified scroll bar |
| unFocus.m | Move focus to the main window |
| volrenAnimationGUI.m | VOLRENANIMATIONGUI MATLAB code for volrenAnimationGUI.fig VOLRENANIMATIONGUI, by itself, creates a new VOLRENANIMATIONGUI or raises the existing singleton* |
| ► ImportExportTools | |
| ► Amira | |
| amiraLabels2bitmap.m | Converts Amira Mesh Labels to bitmap matrix, for Amira ver. 5.2.2 |
| amiraLandmarks2points.m | Read amira landmark coordinates |
| amiraMesh2bitmap.m | Converts Amira Mesh to bitmap matrix [1:height, 1:width, 1:colors, 1:no_stacks] |
| amiraMeshSlice2bitmap.m | Extracts a slice or its subsection from Amira Mesh to bitmap matrix [1:height, 1:width, 1:colors] |
| bitmap2amiraLabels.m | Convert matrix [1:height, 1:width, 1:no_stacks] to Amira Mesh Labels |
| bitmap2amiraMesh.m | Convert bitmap matrix to Amira Mesh binary format |
| getAmiraMeshHeader.m | Get header of Amira Mesh file |
| graph2amiraSpatialGraph.m | Generate Amira Spatial Graph Ascii file |
| ib_amiraImportGui.m | Ib_amiraImportGui function is responsible for a dialog to advanced opening of Amira Mesh files |
| points2amira.m | Generate AM file for Amira with cloud of points, their labels and values |
| points2amiraLandmarks.m | Generate amira Hypersurface Ascii file in: filename - filename to save data points - a matrix with points [point number, x, y, z] options - a structure with additional options .overwrite - 1-automatically overwrite existing files .format - a string with format: binary or ascii |
| points2psi.m | Generate PSI file for Amira the file contains cloud of points, their labels and values |
| surf2amiraHyperSurface.m | Generate amira Hypersurface Ascii file |
| ► export_fig | |
| copyfig.m | COPYFIG Create a copy of a figure, without changing the figure |
| crop_borders.m | CROP_BORDERS Crop the borders of an image or stack of images |
| export_fig.m | EXPORT_FIG Exports figures in a publication-quality format |
| im2gif.m | |
| isolate_axes.m | ISOLATE_AXES Isolate the specified axes in a figure on their own |
| print2array.m | PRINT2ARRAY Exports a figure to an image array |
| using_hg2.m | |
| ► Fiji | |
| fijitest.m | |
| mibFijiSelectDataset.m | MibFijiSelectDataset function is a dialog for selection of datasets from Fiji |
| mibRenderModelFiji.m | Render a model with Fiji engine |
| mibRenderVolumeWithFiji.m | Render 3D volume with Fiji |
| mibStartFiji.m | Start Fiji |
| mibStopFiji.m | Stop Fiji |
| Miji_deploy.m | Modified Miji.m function adapted for the deployed version of im_browser. Mainly the javaaddpath is removed |
| Miji_wrapper.m | A wrapper function to start Miji. Start Fiji in the Matlab and deployed versions of im_browser |
| ► HDF5 | |
| getXMLheader.m | Read XML header for the HDF5 formats (for example, Fiji Big Data Viewer) |
| image2hdf5.m | Save image into hdf5 format |
| loadBigDataViewerFormat.m | Read completely the BigDataViewer format of Fiji into Matlab |
| mibSaveHDF5Dlg.m | MIBSAVEHDF5DLG MATLAB code for mibSaveHDF5Dlg.fig MIBSAVEHDF5DLG, by itself, creates a new MIBSAVEHDF5DLG or raises the existing singleton* |
| p_json.m | DATA = P_JSON(string) This function parses a JSON string and returns a cell array with the parsed data. JSON objects are converted to structures and JSON arrays are converted to cell arrays |
| readBigDataViewerFormat.m | Read completely the BigDataViewer format of Fiji into Matlab |
| saveBigDataViewerFormat.m | Save dataset using the BigDataViewer format of Fiji |
| saveXMLheader.m | Save XML header for the HDF5 formats (for example, Fiji Big Data Viewer) |
| selectHDFSeries.m | SelectHDFSeries function is responsible for selection of series in HDF files |
| struct2xml.m | Convert a MATLAB structure into a xml file [ ] = struct2xml( s, file ) xml = struct2xml( s ) |
| xml2struct.m | Convert xml file into a MATLAB structure [ s ] = xml2struct( file ) |
| ► Imaris | |
| ► @IceImarisConnector | |
| autocast.m | |
| closeImaris.m | |
| createAndSetSpots.m | |
| createDataset.m | |
| display.m | |
| findImaris.m | |
| getAllSurpassChildren.m | |
| getDataSubVolume.m | |
| getDataSubVolumeRM.m | |
| getDataVolume.m | |
| getDataVolumeRM.m | |
| getExtends.m | |
| getImarisVersionAsInteger.m | |
| getMatlabDatatype.m | |
| getSizes.m | |
| getSurpassCameraRotationMatrix.m | |
| getSurpassSelection.m | |
| getVoxelSizes.m | |
| IceImarisConnector.m | |
| indexingStart.m | |
| info.m | |
| isAlive.m | |
| isOfType.m | |
| isSupportedPlatform.m | |
| mapPositionsUnitsToVoxels.m | |
| mapPositionsVoxelsToUnits.m | |
| mapRgbaScalarToVector.m | |
| mapRgbaVectorToScalar.m | |
| mib_setDataSubVolume.m | |
| mib_setDataSubVolumeRM.m | |
| setDataVolume.m | |
| setDataVolumeRM.m | |
| startImaris.m | |
| startImarisServer.m | |
| version.m | |
| imaris_send_data_test.m | |
| mibConnectToImaris.m | Connect to Imaris from Matlab |
| mibGetImarisDataset.m | Get a dataset opened in Imaris and corresponding meta-data |
| mibGetImarisDataset_StandardConnection.m | Get a dataset opened in Imaris and corresponding meta-data |
| mibRenderModelImaris.m | Render a model in Imaris |
| mibSetImarisDataset.m | Send a dataset from MIB to Imaris |
| mibSetImarisSpots.m | Send a spots from MIB to Imaris |
| mibSetImarisSurface.m | Send a surface from MIB to Imaris |
| SurfacesFromSegmentationImage.m | Old surface segmentation function written by Igor Beati from Bitplane |
| ► IMOD | |
| ► @ImodChunk | |
| ► private | |
| genImodChunkStruct.m | |
| freadChunk.m | |
| ImodChunk.m | |
| ► @ImodContour | |
| ► private | |
| genImodContourStruct.m | |
| freadContour.m | |
| getPoints.m | |
| getSurfaceIdx.m | |
| ImodContour.m | |
| setPoints.m | |
| setSurfaceIdx.m | |
| write.m | |
| ► @ImodMesh | |
| ► private | |
| genImodMeshStruct.m | |
| freadMesh.m | |
| ImodMesh.m | |
| ► @ImodModel | |
| ► private | |
| genImodModelStruct.m | |
| openWritable.m | |
| readHeader.m | |
| writeHeader.m | |
| appendObject.m | |
| close.m | |
| draw.m | |
| findRange.m | |
| getDefaultColor.m | |
| getIsFlipped.m | |
| getMax.m | |
| getNObjects.m | |
| getObject.m | |
| getObjectType.m | |
| getPixelSize.m | |
| getPoints.m | |
| getXScale.m | |
| getYScale.m | |
| getZScale.m | |
| ImodModel.m | |
| open.m | |
| setFilename.m | |
| setMax.m | |
| setObject.m | |
| setObjectType.m | |
| setPixelSize.m | |
| setPoints.m | |
| setXScale.m | |
| setYScale.m | |
| setZScale.m | |
| showHeader.m | |
| sortPoints.m | |
| write.m | |
| ► @ImodObject | |
| ► private | |
| genImodObjectStruct.m | |
| writeHeader.m | |
| appendContour.m | |
| freadObject.m | |
| freadObjectMat.m | |
| getColor.m | |
| getContour.m | |
| getDrawSize.m | |
| getNContours.m | |
| getPoints.m | |
| getType.m | |
| ImodObject.m | |
| setColor.m | |
| setContour.m | |
| setDrawSize.m | |
| setName.m | |
| setType.m | |
| showHeader.m | |
| write.m | |
| ► @MRCImage | |
| ► private | |
| default.m | |
| defaultIMODStamp.m | |
| emptyVolume.m | |
| getFileNBytes.m | |
| getModeBytes.m | |
| getReadBytesAsSigned.m | |
| getWriteBytesAsSigned.m | |
| openWritable.m | |
| readHeader.m | |
| setStatisticsFromVolume.m | |
| setVolumeAndHeaderFromVolume.m | |
| writeHeader.m | |
| addLabel.m | |
| addSphere.m | |
| backProject.m | |
| close.m | |
| display.m | |
| getCellX.m | |
| getCellY.m | |
| getCellZ.m | |
| getDimensions.m | |
| getFID.m | |
| getFilename.m | |
| getForceWriteByteMode.m | |
| getHeader.m | |
| getImage.m | |
| getMinAndMaxDensity.m | |
| getModeString.m | |
| getNX.m | |
| getNXStart.m | |
| getNY.m | |
| getNYStart.m | |
| getNZ.m | |
| getNZStart.m | |
| getSlice.m | |
| getStatistics.m | |
| getVolume.m | |
| isVolumeLoaded.m | |
| loadVolume.m | |
| MRCImage.m | |
| normalize.m | |
| open.m | |
| putImage.m | |
| save.m | |
| setFilename.m | |
| setForceWriteByteMode.m | |
| setNZ.m | |
| setPixelSize.m | |
| setSubvolume.m | |
| setVolume.m | |
| showHeader.m | |
| writeEM.m | |
| writeVTK.m | |
| zero.m | |
| ► Visualization | |
| cntShow.m | |
| fitImage.m | |
| showMovie.m | |
| showMRCContour.m | |
| showMRCImage.m | |
| stackGallery.m | |
| volShow.m | |
| em2mrc.m | |
| getMRCfile.m | Read data in MRC/REC format |
| getMRCheader.m | Read header of MRC/REC file |
| mibExportModelToImodModel.m | Export model to Imod model type |
| writeAndCheck.m | |
| ► nrrd | |
| bitmap2nrrd.m | Save bitmap matrix to NRRD format |
| compilethis.m | |
| get_nrrd_metadata.m | Get metadata for a NRRD dataset |
| ib_image2nrrd.m | Save image to NRRD binary format |
| nrrdLoadWithMetadata.c | |
| nrrdLoadWithMetadata.m | |
| nrrdSaveWithMetadata.c | |
| nrrdSaveWithMetadata.m | |
| ► Omero | |
| mibOmeroLoginDlg.m | Varargout = mibOmeroLoginDlg(varargin) mibOmeroLoginDlg function is responsible for login to OMERO server |
| generateSequentialFilename.m | Generate sequential filenames |
| mib_uigetfile.m | Wrapper function to provide a modified uigetfile dialog for MacOS Catalina. The general syntax is the same as for uigetfile, except missing MultiSelect key |
| mibGetImageMetadata.m | Get metadata for images |
| mibGetImages.m | Generate image dataset from the files structure and the img_info containers.Map |
| mibImage2jpg.m | Save image in JPG format, 2D slices |
| mibImage2mrc.m | Export volume in MRC format |
| mibImage2png.m | Save image in PNG format, 2D slices |
| mibImage2tiff.m | Save image in TIF format, 2D slices or 3D stacks |
| mibImWrite.m | Save image to a file using Matlab imwrite function |
| mibLoadImages.m | Load images from the list of files |
| stlwrite.m | STLWRITE Write STL file from patch or surface data |
| xlwrite.m | XLWRITE Write to Microsoft Excel spreadsheet file using Java XLWRITE(FILE,ARRAY) writes ARRAY to the first worksheet in the Excel file named FILE, starting at cell A1. It aims to have exactly the same behaviour as XLSWRITE. See also XLSWRITE |
| ► jars | |
| ► xlwrite | |
| Test_xlWrite.m | % Small demonstration on how to use XLWRITE |
| xlwrite.m | XLWRITE Write to Microsoft Excel spreadsheet file using Java XLWRITE(FILE,ARRAY) writes ARRAY to the first worksheet in the Excel file named FILE, starting at cell A1. It aims to have exactly the same behaviour as XLSWRITE. See also XLSWRITE |
| ► MIB_Mac_resources | |
| addSpkgBinPath.m | |
| ► techdoc | |
| ► config | |
| class_substitutes.c | |
| developers.c | |
| ► Tools | |
| ► CellMigration | |
| cellMigration.m | |
| gaussF.m | GAUSS produces an N-dimensional gaussian function (N=1,2,3) |
| padData.m | --------------------------------------------------------------— ---— Author : Constantino Carlos Reyes-Aldasoro----------— ---— PHD the University of Warwick----------— ---— Supervisor : Abhir Bhalerao ---------------------— |
| reduceu.m | |
| traceTransform_old.m | |
| zerocross.m | |
| ► Frangi | |
| eig2image.m | This function eig2image calculates the eigen values from the hessian matrix, sorted by abs value. And gives the direction of the ridge (eigenvector smallest eigenvalue) |
| eig3volume.c | |
| eig3volume.m | |
| FrangiFilter2D.m | This function FRANGIFILTER2D uses the eigenvectors of the Hessian to compute the likeliness of an image region to vessels, according to the method described by Frangi:2001 (Chapter 2) |
| FrangiFilter3D.m | |
| Hessian2D.m | This function Hessian2 Filters the image with 2nd derivatives of a Gaussian with parameter Sigma |
| Hessian3D.m | This function Hessian3D filters the image with an Gaussian kernel followed by calculation of 2nd order gradients, which aprroximates the 2nd order derivatives of the image |
| imgaussian.c | |
| imgaussian.m | IMGAUSSIAN filters an 1D, 2D color/greyscale or 3D image with an Gaussian filter. This function uses for filtering IMFILTER or if compiled the fast mex code imgaussian.c . Instead of using a multidimensional gaussian kernel, it uses the fact that a Gaussian filter can be separated in 1D gaussian kernels |
| ► HistThresh | |
| A.m | X = A(y,j) |
| B.m | X = B(y,j) |
| bimodtest.m | B = bimodtest(y) |
| C.m | X = C(y,j) |
| D.m | X = D(y,j) |
| flocmax.m | Y = flocmax(x) |
| hbalance.m | E = hbalance(y,ind) |
| hconvhull.m | H = hconvhull(h) |
| th_concavity.m | T = th_concavity(I,n) |
| th_entropy.m | T = th_intermeans(I,n) |
| th_intermeans.m | T = th_intermeans(I,n) |
| th_intermeans_iter.m | T = th_intermeans_iter(I,n) |
| th_intermodes.m | T = th_intermodes(I,n) |
| th_maxlik.m | T = th_maxlik(I,n) |
| th_mean.m | T = th_mean(I,n) |
| th_median.m | T = th_median(I,n) |
| th_minerror.m | T = th_minerror(I,n) |
| th_minerror_iter.m | T = th_minerror_iter(I,n) |
| th_minimum.m | T = th_minimum(I,n) |
| th_moments.m | T = th_moments(I,n) |
| th_ptile.m | T = th_ptile(I,p,n) |
| ► matGeom | |
| ► geom2d | |
| clipEdge.m | CLIPEDGE Clip an edge with a rectangular box |
| distancePoints.m | DISTANCEPOINTS Compute distance between two points |
| minDistancePoints.m | MINDISTANCEPOINTS Minimal distance between several points |
| ► geom3d | |
| clipEdge3d.m | CLIPEDGE3D Clip a 3D edge with a cuboid box |
| clipLine3d.m | CLIPLINE3D Clip a line with a box and return an edge |
| crossProduct3d.m | CROSSPRODUCT3D Vector cross product faster than inbuilt MATLAB cross |
| intersectLinePlane.m | INTERSECTLINEPLANE Intersection point between a 3D line and a plane |
| linePosition3d.m | LINEPOSITION3D Return the position of a 3D point projected on a 3D line |
| triangulateCurvePair.m | TRIANGULATECURVEPAIR Compute triangulation between a pair of 3D curves |
| trimeshSurfaceArea.m | TRIMESHSURFACEAREA Surface area of a triangular mesh |
| vectorCross3d.m | VECTORCROSS3D Vector cross product faster than inbuilt MATLAB cross |
| vectorNorm3d.m | VECTORNORM3D Norm of a 3D vector or of set of 3D vectors |
| ► mibDeepSupport | |
| customDiceForwardLoss.m | Loss = customDiceForwardLoss(Y, T, dataDimension, useClasses) returns the Dice loss between the predictions Y and the training targets T |
| exportONNXNetwork.m | ExportONNXNetwork Export network or graph of layers to ONNX model format |
| matReadInstanceLabels.m | Read preprocessed instance segmentation labels and return them as a cell array with 3 element |
| mibDeepAugmentAndCrop2dPatchMultiGPU.m | |
| mibDeepAugmentAndCrop3dPatchMultiGPU.m | |
| mibDeepConvertOldAugmentationSettingsToNew.m | Supporting function for DeepMIB, the function converts old augmentation settings to the new set of settings from MIB 2.8455 |
| mibDeepCustomTrainingProgressDisplay.m | |
| mibDeepCustomTrainingProgressDisplayTrainNet.m | |
| mibDeepGenerateDefaultAugmentationSettings.m | Generate default augmentation settings from MIB 2.8455 |
| mibDeepSaveTrainingPlot.m | Save custom training plot to a file |
| mibDeepStopTrainingCallback.m | Stop training process by pressing the Stop training or Emergency stop buttons |
| mibDeepStopTrainingWithoutPlots.m | Stop training, when it is done without the training plot |
| mibDeepStoreLoadCategorical.m | Supporting function for mibDeepController read categorical dataset and return it as a cell similar to pixelLabelDatastore |
| mibDeepStoreLoadImages.m | Supporting function for mibDeepController load image function for the imagedatastore |
| mibDeepStoreLoadModel.m | Supporting function for mibDeepController to be used with pixelLabelDatastore to load MIB models |
| mibDeepTrainingProgressStructUpdateAxesLimits.m | Function to handle callbacks from the context menu for mibDeepTrainingProgressStruct.UILossAxes |
| saveInstanceLabelsParFor.m | SaveInstanceLabelsParFor(fn, imageFilename, instanceBoxes, instanceNames, instanceMasks, compressModels) saving from parfor loop converted labels for training of 2D instance segmentation as it is not possible to use save directly inside parfor. This function is used in mibDeepController.processImagesForInstanceSegmentation to preprocess instance labels |
| ► prettify_MATLAB_html | |
| ► publish overload | |
| publish.m | |
| ► RandomForest | |
| ► MembraneDetection | |
| centeredRotate.m | |
| filterImageWithMembraneTemplateRotated.m | Filter image with a rotated template |
| filterSmallRegions.m | |
| gradientImg.m | |
| imsmooth.m | |
| makeColorOverlay.m | |
| meanvar.c | |
| membraneFeatures.m | Normalize image contrast cpuParallelLimit - number of parallel CPUs to use |
| norm01.m | |
| normxcorr2_mex.m | |
| script_for_grayscale_distribution.m | |
| shiftDown.m | |
| shiftLeft.m | |
| shiftRight.m | |
| shiftUp.m | |
| skeletonize.m | |
| skript_applyClassifier_to_all_images.m | Author: Verena Kaynig load forest file |
| skript_extractMembraneFeatures_for_allImages.m | Author: Verena Kaynig save feature matrizes |
| skript_trainClassifier_for_membraneDetection.m | Author: Verena Kaynig this you can change |
| structureTensorImage2.m | |
| transformImageFast.c | |
| uint8Img.m | |
| ► RF_Class_C | |
| ► src | |
| classRF.cpp | |
| classTree.cpp | |
| cokus.cpp | |
| cokus_test.cpp | |
| mex_ClassificationRF_predict.cpp | |
| mex_ClassificationRF_train.cpp | |
| qsort.c | |
| rf.h | |
| rfutils.cpp | |
| twonorm_C_wrapper.cpp | |
| classRF_predict.m | |
| classRF_train.m | |
| compile_linux.m | |
| compile_windows.m | |
| test_ClassRF_extensively.m | Run plethora of tests |
| tutorial_ClassRF.m | A simple tutorial file to interface with RF Options copied from http://cran.r-project.org/web/packages/randomForest/randomForest.pdf |
| ► RF_Reg_C | |
| ► src | |
| cokus.cpp | |
| cokus_test.cpp | |
| diabetes_C_wrapper.cpp | |
| mex_regressionRF_predict.cpp | |
| mex_regressionRF_train.cpp | |
| qsort.c | |
| reg_RF.cpp | |
| reg_RF.h | |
| compile_linux.m | |
| compile_windows.m | |
| regRF_predict.m | Requires 2 arguments X: data matrix model: generated via regRF_train function |
| regRF_train.m | Requires 2 arguments and the rest 2 are optional X: data matrix Y: target values ntree (optional): number of trees (default is 500) mtry (default is max(floor(D/3),1) D=number of features in X) |
| test_RegRF_extensively.m | ************************************************************** |
| tutorial_RegRF.m | A simple tutorial file to interface with RF Options copied from http://cran.r-project.org/web/packages/randomForest/randomForest.pdf |
| ► RegionGrowing | |
| regiongrowing.m | REGIONGROWING A MEXed 2D/3D region growing algorithm |
| RegionGrowing_mex.cpp | |
| ► Supervoxels | |
| ► maxflow-v2.22 | |
| ► adjacency_list | |
| block.h | |
| graph.cpp | |
| graph.h | |
| maxflow.cpp | |
| ► adjacency_list_new_interface | |
| block.h | |
| graph.cpp | |
| graph.h | |
| maxflow.cpp | |
| ► forward_star | |
| block.h | |
| graph.cpp | |
| graph.h | |
| maxflow.cpp | |
| compile_c_files.m | Compile all c files |
| drawregionboundaries.m | |
| maskimage.m | |
| maxflow.m | |
| maxflow_v222.m | |
| maxflowmex_v222.cpp | |
| slicmex.c | |
| slicomex.c | |
| slicsupervoxelmex.c | |
| slicsupervoxelmex_byte.c | |
| anisodiff.m | ANISODIFF - Anisotropic diffusion |
| bwdistsc.m | D=BWDISTSC(BW,ASPECT) BWDISTSC computes Euclidean distance transform of a binary 3D image BW. Distance transform assigns to each pixel in BW a number that is the distance from that pixel to the nearest nonzero pixel in BW. BWDISTSC can accept a regular 2D image, a 3D array, and a cell array of 2D slices. ASPECT is a 3-component vector defining the voxel-aspect-ratio for BW. If ASPECT is not given, [1 1 1] isotropic aspect ratio is assumed |
| bwdistsc1.m | D=BWDISTSC1(BW,ASPECT,MAXVAL) BWDISTSC1 computes Euclidean distance transform of a binary 3D image BW out to a specified value MAXVAL. This allows accelerating the calculations in some cases with strongly nonconvex geometries, if the distance transform only needs to be calculated out to a specific value. The distance transform assigns to each pixel in BW a number that is the distance from that pixel to the nearest nonzero pixel in BW. BW may be a 3D array or a cell array of 2D slices. BWDISTSC1 can also accept regular 2D images. ASPECT is a 3-component vector defining the aspect ratios to use when calculating the distances in BW. If ASPECT is not set, isotropic aspect ratio [1 1 1] is used. If MAXVAL is specified, the distance transform will be only calculated out to the value MAXVAL |
| cell2clip.m | Cell2clip copies contents of cell-array to the clipboard |
| convertAbsoluteToRelativePath.m | Convert absolute path into relative path, where the part of the absolute path that is matching the relative path is replaced with the templateText |
| convertPixelsToUnits.m | Convert pixel with x, y, z coordinate to the physical imaging units |
| convertRelativeToAbsolutePath.m | Convert relative path into absolute path, where the part of the relative path containing text template (templateText) will be replaced with the abosolute path |
| DnD_uifigure.m | Set up a callback when file/folder is dropped onto a uifigure component |
| editbox_Callback.m | Check for entered values in an edit box |
| findjobj.m | Findjobj Find java objects contained within a specified java container or Matlab GUI handle |
| findNode.m | Find a node in the uitree which has nodeName text in it, used by mibDatasetInfoController |
| fstack.m | Focus stacking |
| fstack_mib.m | Extended depth-of-field focus stacking based on fstack function by Said Pertuz https://se.mathworks.com/matlabcentral/fileexchange/55115-extended-depth-of-field Generate extended depth-of-field image from focus sequence using noise-robust selective all-in-focus algorithm [1] |
| generateBoxPlot.m | Generate a box plot with points |
| generateDefaultKeyShortcuts.m | Generate KeyShortcuts structure with defauld key shortcuts |
| GetExeLocation.c | |
| getPrefDir.m | Get directory where MIB preferences are stored on Windows it is C:\Users\Username\Matlab on Mac it is /Users/username/Matlab on Linux it is /home/username/Matlab |
| ginputc.m | GINPUTC Graphical input from mouse. GINPUTC behaves similarly to GINPUT, except you can customize the cursor color, line width, and line style |
| imclipboard.m | IMCLIPBOARD Copy and paste images to and from system clipboard |
| imRAG.m | IMRAG Region adjacency graph of a labeled image |
| imRichRAG.m | IMRICHRAG Region adjacency graph of a labeled image with edge infos, originating from the imRAG function |
| mib_compile_c_files.m | This script will compile all the C files get MIB directory |
| mibAddScaleBar.m | I = mibAddScaleBar(I, pixSize, scale, orientation, scaleBarHeight) add a scale bar to the image. Requires insertText and insertMarker functions from the Computer Vision System Toolbox. When these functions are not available is using an old function |
| mibAddText2Img.m | Add text label to the image, a new function introduced in MIB 2.22. Requires insertText and insertMarker functions from the Computer Vision System Toolbox. When these functions are not available mibAddText2Img is using an old function |
| mibAddText2Img_Legacy.m | Add text label to the image, an older function that does not use insertText and insertMarker functions from the Computer Vision System Toolbox |
| mibAlignmentDetectFeatures.m | Detect feature points for image, this function is used in AutomaticFeatureBasedAlignment function in mibAlignmentController |
| mibCalcCurveLength.m | Calculate length of the curve objects in the slice |
| mibCalcShifts.m | Calculate alignment shifts between slices in I |
| mibConcatenateStructures.m | Update fields of primaryStruct using the fields of secondaryStruct |
| mibConnectPoints.m | Generate a bitmap image with lines that connect points (pnts) |
| mibCrossShiftStack.m | ImgOut = mibCrossShiftStack(imgIn, shiftsX, shiftsY, options) Shift stack provided in imgIn using translation numbers in shiftX and shiftY |
| mibCrossShiftStacks.m | [imgOut, bbShiftXY] = mibCrossShiftStacks(I1, I2, shiftX, shiftY) Shift I2 vs I1 using translation numbers in shiftX and shiftY |
| mibDoAndiffFiltering.m | Filter dataset with anisotropic diffusion |
| mibDoImageFiltering.m | Filter image with basic Matlab filters |
| mibDoImageFiltering2.m | Filter the image, alternative version of mibDoImageFiltering with more filters and BatchOpt compatible structure |
| mibElasticDistortionFilter.m | Apply elastic deformations to img, the code is based on Best Practices for Convolutional Neural Networks Applied to Visual Document Analysis by Patrice Y. Simard, Dave Steinkraus, John C. Platt http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.160.8494&rep=rep1&type=pdf https://cognitivemedium.com/assets/rmnist/Simard.pdf and codes available at |
| mibGenerateDefaultSegmentationPalette.m | Generate color palette depending on the provided paletteName and required noColors |
| mibGetFrangiMask.m | Return Frangi mask generated from img |
| mibGetMorphMask.m | Return result of BW Morphological filters generated from img |
| mibGetStrelMask.m | Return Strel mask (imtophat/imbothat) generated from the img |
| mibGetVersionNumberic.m | Get MIB version in numeric format from the string |
| mibImageProfileIntegrate.m | Calculate image intensity profile for line ROI based on code by Damien in comments of http://se.mathworks.com/matlabcentral/fileexchange/11568-extract-integrated-intensity-profiles-from-image |
| mibInterpolateLines.m | Interpolate lines between the slices |
| mibInterpolateShapes.m | Interpolate the shapes between the slices |
| mibOscResampling.m | Resample image usng OSC method |
| mibRemoveBranches.m | Remove branches from thinned bitmap image img the line can be thinned using _img = bwmorph(img, thin, Inf)_ command somewhat based on "Exploring shortest paths – part 5" by Steve Eddins (https://blogs.mathworks.com/steve/2011/12/13/exploring-shortest-paths-part-5/) |
| mibRemoveSaltAndPepperNoise.m | |
| mibRenderModel.m | Render a model using isosurfaces |
| mibResize3d.m | Resize 3D dataset |
| mibRunningAverageSmoothPoints.m | MibRunningAverageSmoothPoints - Smooth points for running average correction |
| mibSaveTableToHeaderCSV.m | Save MATLAB Table (T) to CSV file (fn) with a header standard MATLAB writetable function does not support generation of headers, this function allows to produce CSV file with header generated from table Properties |
| mibShowErrorDialog.m | Show error that is generated in try/catch blocks |
| mibSubtractRunningAverage.m | Smooth drift correction using the running average correction |
| mibTraceCurve.m | Connect points with search for a minimum gradients |
| num2clip.m | |
| parseStructToTree.m | Function to parse structure (XML) to uitree object based on struct2xml.m file by W. Falkena, ASTI, TUDelft, 27-08-2010 |
| patchnormals.m | This function PATCHNORMALS calculates the normals of a triangulated mesh. PATCHNORMALS calls the patchnormal_double.c mex function which first calculates the normals of all faces, and after that calculates the vertice normals from the face normals weighted by the angles of the faces |
| patchnormals_double.c | |
| patchnormals_double.m | |
| regionprops3mib.m | Regionprops3mib measures the geometric properties of image objects in 3D space. Objects are defined as connected pixels in 3D. This function uses regionprops to get pixellist from the binary image. If you'd like to define objects connectivity on our own, use bwlabeln first |
| saveImageParFor.m | SaveImageParFor(fn, imgOut, compressImage) saving image from parfor loop as it is not possible to use save directly inside parfor this function is used in mibDeepController to preprocess images |
| showErrorDialog.m | Show error that is generated in try/catch blocks |
| struct2array.m | Replacement for struct2array function that was present is Matlab before R2021b (at least) |
| uigetfile_n_dir.m | Pick multiple directories and/or files |
| updateBatchOptCombineFields_Shared.m | Common function used by all tools compatible with the Batch mode to combine fields of the input structure BatchOptIn with fields of the default structure BatchOpt |
| updateBatchOptFromGUI_Shared.m | Common function used by all tools compatible with the Batch mode to update BatchOpt structure fields from GUI widgets |
| updateGUIFromBatchOpt_Shared.m | Common function used by all tools compatible with the Batch mode to setup widgets of GUI from the BatchOpt structure |
| view3d.m | View3d Interactively rotate, zoom and pan the view of a 3-D plot |
| violin.m | |
| windv.m | Windv(vector, window size, asInSmooth) vectorized version of windv() smooths a vector using a window of +/- window size window size is reduced at the edges |
| xlswrite2.m | XLSWRITE Stores numeric array or cell array in Excel workbook |
| xlswrite3.m | XLSWRITE Stores numeric array or cell array in Excel workbook |
| mib.m | |
| mib_deploy.m | Following wrapper is needed for mib |
1.13.2