  Classes | |
 @imageData | |
  addColorChannel.m | |
| clearContents.m | |
| clearMask.m | |
| clearSelection.m | |
| convertDataToMouseCoordinates.m | |
| convertImage.m | |
| convertModel.m | |
| convertMouseToDataCoordinates.m | |
| copyColorChannel.m | |
| createModel.m | |
| cropDataset.m | |
| deleteColorChannel.m | |
| deleteSlice.m | |
| generateModelColors.m | |
| getBoundingBox.m | |
| getCoordinatesOfShownImage.m | |
| getCurrentSlice.m | |
| getCurrentSliceNumber.m | |
| getCurrentTimePoint.m | |
| getData2D.m | |
| getData3D.m | |
| getData4D.m | |
| getDataset.m | |
| getDatasetDimensions.m | |
| getDatasetSizeInBytes.m | |
| getFullSlice.m | |
| getMaterialNames.m | |
| getRGBimage.m | |
| getRoiCrop.m | |
| getRoiCropSlice.m | |
| getSlice.m | |
| getSliceToShow.m | |
| imageData.m | |
| insertEmptyColorChannel.m | |
| insertSlice.m | |
| invertColorChannel.m | |
| mark2selection.m | |
| moveMaskToSelectionDataset.m | |
| moveModelToMaskDataset.m | |
| moveModelToSelectionDataset.m | |
| moveSelectionToMaskDataset.m | |
| moveSelectionToModelDataset.m | |
| moveView.m | |
| plotImage.m | |
| replaceDataset.m | |
| replaceImageColor.m | |
| resizeImage.m | |
| rotateColorChannel.m | |
| setCurrentSlice.m | |
| setData2D.m | |
| setData3D.m | |
| setData4D.m | |
| setDataset.m | |
| setFullSlice.m | |
| setMaterialNames.m | |
| setRoiCrop.m | |
| setRoiCropSlice.m | |
| setSlice.m | |
| setSliceToShow.m | |
| swapColorChannels.m | |
| transpose.m | |
| updateAxesLimits.m | |
| updateBoundingBox.m | |
| updateDisplayParameters.m | |
| updateImgInfo.m | |
 updateParameters.m | |
| @imageUndo | |
| imageUndo.m | |
| @Labels | |
| Labels.m | |
| @Measure | |
| Measure.m | |
 @roiRegion | |
 roiRegion.m | |
| GuiTools | |
| volren | |
| affine_transform_2d_double.m | Affine transformation function (Rotation, Translation, Resize) This function transforms a volume with a 3x3 transformation matrix |
| getRGBvolume.m | Generate RGB volume rendering image of the stack |
| 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 |
| volren_scrollWheelFcn.m | |
| volren_WindowButtonDownFcn.m | |
| volren_WindowButtonUpFcn.m | |
| volren_WindowInteractMotionFcn.m | |
| volren_winMouseMotionFcn.m | Change cursor shape when cursor is inside the axis |
| volrenToolbarSwitch_ClickedCallback.m | |
| backgroundRemovalGUI_Callback.m | Callback to action done with the handles.backgroundPanel |
| backgroundStrelSmoothingChk_Callback.m | Callback to the handles.backgroundStrelSmoothingChk |
| brushSuperpixelsCheck.m | — Executes on button press in brushSupervoxelsCheck |
| bufferToggles_cb.m | A callback function for the popup menu of the buffer buttons in the upper part of the Directory contents panel. This callback is triggered from all those buttons |
| changelayerEdit_Callback.m | A callback for changing the slices of the 3D dataset by entering the new slice number |
| changelayerSlider_Callback.m | A callback function for handles.changelayerSlider. Responsible for showing next or previous slice of the dataset |
| changeTimeEdit_Callback.m | A callback for changing the time points of the dataset by entering a new time value |
| changeTimeSlider_Callback.m | A callback function for handles.changeTimeSlider. Responsible for showing next or previous time point of the dataset |
| channelMixerTable_CellSelectionCallback.m | A cell selection callback function function for the handles.ib_channelMixerTable table |
| createModelBtn_Callback.m | Create Model |
| editbox_Callback.m | Check for entered values in an edit box and switch the focus to handles.updatefilelistBtn |
| filesListboxContext_cb.m | Context menu to the to the handles.filesListbox, the menu is called with the right mouse button |
| getClickPoint.m | A function that gets ginput function to pick a point within imageAxes |
| ib_aboutDlg.m | IB_ABOUTDLG MATLAB code for ib_aboutDlg.fig IB_ABOUTDLG, by itself, creates a new IB_ABOUTDLG or raises the existing singleton* |
| ib_addIcons.m | Add icons to the menus |
| ib_channelMixerTable_Callback.m | A callback function for the handles.ib_channelMixerTable table |
| ib_checkUpdate.m | IB_CHECKUPDATE MATLAB code for ib_checkUpdate.fig IB_CHECKUPDATE, by itself, creates a new IB_CHECKUPDATE or raises the existing singleton* |
| ib_cropGui.m | Ib_cropGui function is responsible for the crop of dataset |
| ib_datasetInfoGui.m | Ib_datasetInfoGui is a GUI window that shows parameters of the dataset |
| ib_do_backup.m | Store the dataset for Undo |
| ib_do_undo.m | Undo the recent changes with Ctrl+Z shortcut |
| ib_getDataset.m | Get complete 4D volume of the dataset, a wrapper function |
| ib_getSlice.m | Get the 2D slice from the dataset, the wrapper function |
| ib_getStack.m | Get the 3D volume from the dataset, a wrapper function |
| ib_labelsGui.m | Ib_labelsGui is a GUI tool to show list of labels |
| ib_moveLayers.m | To move information between the layers |
| ib_resampleGui.m | Ib_resampleGui function is responsible for resampling of datasets |
| ib_setDataset.m | Update complete 4D volume of the dataset, a wrapper function |
| ib_setSlice.m | Update the 2D slice of the dataset, the wrapper function |
| ib_setStack.m | Update a 3D stack of the dataset, a wrapper function |
| ib_updateCursor.m | Handles = ib_updateCursor(handles, mode) Update brush cursor |
| ib_updateFontSize.m | Update font size for text widgets |
| im_browser_brush_scrollWheelFcn.m | Control callbacks from mouse scroll wheel during the brush tool |
| im_browser_CloseRequestFcn.m | — Executes when user attempts to close im_browser |
| im_browser_filesListbox_Callback.m | Im_browser_filesListbox_Callback(hObject, eventdata, handles) navigation in the file list, i.e. open file or change directory |
| im_browser_panAxesFcn.m | This function is responsible for moving image during panning |
| im_browser_PanelShiftBtnUpFcn.m | This is callback for the release of a mouse button over handles.separatingPanel to change size of Directory contents and Segmentation panels |
| im_browser_ResizeFcn.m | Resizing for panels of MIB |
| im_browser_scrollWheelFcn.m | Control callbacks from mouse scroll wheel |
| im_browser_WindowBrushMotionFcn.m | This function draws the brush trace during use of the brush tool |
| im_browser_WindowButtonDownFcn.m | This is callback for the press of a mouse button |
| im_browser_WindowButtonUpFcn.m | Callback for release of the mouse button |
| im_browser_WindowKeyPressFcn.m | HObject handle to im_browser (see GCBO) eventdata structure with the following fields (see FIGURE) Key: name of the key that was released, in lower case Character: character interpretation of the key(s) that was released Modifier: name(s) of the modifier key(s) (i.e., control, shift) released handles structure with handles and user data (see GUIDATA) disp(eventdata.Key); disp(eventdata.Character); disp(eventdata.Modifier); |
| im_browser_WindowKeyPressFcn_BrushSuperpixel.m | Function to check key callbacks when using the Brush in the Superpixel mode hObject handle to im_browser (see GCBO) eventdata structure with the following fields (see FIGURE) Key: name of the key that was released, in lower case Character: character interpretation of the key(s) that was released Modifier: name(s) of the modifier key(s) (i.e., control, shift) released handles structure with handles and user data (see GUIDATA) disp(eventdata.Key); disp(eventdata.Character); disp(eventdata.Modifier); |
| im_browser_WindowKeyReleaseFcn.m | HObject handle to im_browser (see GCBO) eventdata structure with the following fields (see FIGURE) Key: name of the key that was released, in lower case Character: character interpretation of the key(s) that was released Modifier: name(s) of the modifier key(s) (i.e., control, shift) released handles structure with handles and user data (see GUIDATA) |
| im_browser_winMouseMotionFcn.m | Returns coordinates and image intensities under the mouse cursor |
| imAdjustBtn_Callback.m | Open image adjustments dialog |
| imAdjustments.m | ImAdjustments function allows to adjust contrast and gamma of the shown dataset |
| imageFilterDoitBtn_Callback.m | Callback to the handles.imageFilterDoitBtn, filters image with the selected filter |
| imageFilterPopup_Callback.m | Callback to the handles.imageFilterPopup, modifies panels with respect to the selected filter type |
| imfiltPar1Edit_Callback.m | Callback to the handles.imfiltPar1Edit, checks parameters for image filters |
| imfiltPar2Edit_Callback.m | Callback to the handles.imfiltPar2Edit, checks parameters for image filters |
| loadModelBtn_Callback.m | Callback to the handles.loadModelBtn, loads model to MIB from a file |
| localNormSigmaSlider_Callback.m | Callback to the handles.localNormSigmaSlider |
| logList.m | LogList function calls a window with Log list of actions that were performed with the dataset |
| magicwandMethodPopup_Callback.m | Callback to the handles.magicwandMethodPopup, allowing selection of method for the MagicWand-RegionGrowing tool |
| maskShowCheck_Callback.m | Callback to the handles.maskShowCheck, allows to toggle visualization of the mask layer |
| menuDatasetAlignDatasets.m | Callback to Menu->Dataset->Alignment tool align the dataset or stitch several datasets |
| menuDatasetBoundingBox.m | Callback to Menu->Dataset->Bounding Box... set manually the parameters for the bounding box |
| menuDatasetCrop.m | Callback to Menu->Dataset->Crop dataset... starts the Crop dialog |
| menuDatasetResample.m | Callback to Menu->Dataset->Resample... starts the Resample dialog |
| menuDatasetSlice.m | Callback to Menu->Dataset->Slice do actions with individual slices |
| menuDatasetTransform.m | Callback to Menu->Dataset->Transform... do different transformation with the dataset |
| menuFileChoppedImage.m | Callback to Menu->File->Chopped Images, imports/exports large datasets from/to smaller datasets |
| menuFileExportImage.m | Callback to the handles.menuFileExportImage, exports image and meta-data from MIB to the main Matlab workspace or Imaris |
| menuFileImportImage.m | Callback to Menu->File->Import Image, imports model from Matlab main workspace or system clipboard |
| menuFileMakeMovie.m | Callback to Menu->File->Make movie, renders a movie file |
| menuFileOmeroImport.m | Callback to Menu->File->OMERO Import, imports data from OMERO server |
| menuFilePreferences.m | Callback to Menu->File->Preferences, opens the Preferences dialog |
| menuFileSaveImageAs.m | Callback to the handles.menuFileSaveImageAs, saves image to a file |
| menuFileSnapshot.m | Callback to Menu->File->Make snapshot, renders a snapshot of the shown area |
| menuImageColorCh.m | Callback to Menu->Image->Color Channels do actions with individual color channels |
| menuImageContrast.m | Callback to Menu->Image->Contrast do contrast enhancement |
| menuImageConvert.m | Callback to the Menu->Image->Mode, convert image to different formats |
| menuImageIntensity.m | Callback to Menu->Image->Intensity Profile get intensity values |
| menuImageMode.m | Callback to the Menu->Image->Mode, convert image to different formats |
| menuImageProfileArbitrary_Callback.m | Callback to the handles.menuImageProfileLine, generates a profile of image intensities under an arbitrary line |
| menuImageProfileLine_Callback.m | Callback to the handles.menuImageProfileLine, generates a profile of image intensities under a line |
| menuMaskImport.m | Callback to Menu->Mask->Import imports the Mask layer from the main Matlab workspace |
| menuMaskInvert.m | Callback to Menu->Mask->Invert inverts the Mask layer |
| menuMaskLoad.m | Callback to Menu->Mask->Load Mask loads the Mask layer to MIB from a file |
| menuMaskSaveAs.m | Callback to Menu->Mask->Save As saves the Mask layer to a file |
| menuModelFillMembrane.m | Callback to Menu->Model->FillMembrane an experimental function to extend membranes such that the membranes are connected between the slices and holes are eliminated |
| menuModelsExport.m | Callback to Menu->Models->Export export the Model layer to the main Matlab workspace |
| menuModelsImport.m | Callback to Menu->Models->Import imports the Model layer from the main Matlab workspace |
| menuModelsSaveAs.m | Callback to Menu->Models->Save as saves model to a file |
| menuSelectionBuffer.m | Callback to Menu->Selection to Buffer... Copy/Paste/Clear of the selection of the shown layer |
| menuSelectionBufferCopy_Callback.m | Store the selection from the current layer to a buffer |
| menuSelectionInterpolate.m | Callback to the Menu->Selection->Interpolate; interpolates shapes of the selection layer |
| menuSelectionInvert.m | Callback for Menu->Selection->Invert invert selection layer |
| menuSelectionToMaskBorder.m | Callback to Menu->Selection->Expand to Mask border expand selection to borders of the Masked layer |
| menuToolsMeasure.m | Callback to Menu->Tools->Measure length |
| mib_BoundingBoxDlg.m | Custom input dialog |
| mib_calibrateScaleBar.m | Obtain physical X and Y size of pixels using a scale bar plotted on the loaded image |
| mib_contrastContext_cb.m | Adjust contrast context menu callback |
| mib_inputdlg.m | Custom input dialog |
| mib_keyShortcutsDlg.m | MIB_KEYSHORTCUTSDLG MATLAB code for mib_keyShortcutsDlg.fig MIB_KEYSHORTCUTSDLG, by itself, creates a new MIB_KEYSHORTCUTSDLG or raises the existing singleton* |
| mib_measureTool.m | MIB_MEASURETOOL MATLAB code for mib_measureTool.fig MIB_MEASURETOOL, by itself, creates a new MIB_MEASURETOOL or raises the existing singleton* |
| mib_rescaleWidgets.m | Rescale widgets for different operating systems |
| model_cm_Callback.m | Context menu to the to the handles.segmList (Materials list of the Segmentation panel), the menu is called with the right mouse button |
| modelShowCheck_Callback.m | Toggle the Model layer on/off |
| pixInfo_cb.m | Center image to defined position it is a callback from a popup menu above the pixel information field of the Path panel |
| preferencesDlg.m | Varargout = preferencesDlg(varargin) preferencesDlg a dialog responsible for setting preferences for im_browser.m |
| redrawChannelMixerTable.m | Update handles.channelMixerTable table and handles.ColChannelCombo color combo box |
| removeMaterialBtn_Callback.m | Callback to the handles.removeMaterialBt, removes selected material from the model |
| roiAddBtn_Callback.m | Callback to the handles.roiAddBtn, adds a roi to a dataset |
| roiList_cm_Callback.m | Context menu to the to the handles.roiList, the menu is called with the right mouse button |
| roiLoadBtn_Callback.m | Callback to the handles.roiLoadBtn, loads roi from a file to MIB |
| roiRemoveBtn_Callback.m | Callback to the handles.roiRemoveBtn, removes selected roi from a list of rois |
| roiRoiToSelectionBtn_Callback.m | Callback from the ROI to Selection button in the ROI panel to copy areas under the shown ROIs to the Selection layer |
| roiSaveBtn_Callback.m | Callback to the handles.roiSaveBtn, saves roi to a file using matlab format |
| roiShowCheck_Callback.m | Toggle show/hide state of ROIs, as callback of handles.roiShowCheck |
| roiTypePopup_Callback.m | Callback for selection of the handles.roiTypePopup combo box with selection of ROI type to add |
| saveModelToolbar_ClickedCallback.m | Callback to the handles.saveModelToolbar, saves the model in the matlab format to the specified file |
| scrollbarClick_Callback.m | This is callback for the press of a mouse button above specified scroll bar |
| segmSelectedOnlyCheck_Callback.m | Callback to the handles.segmSelectedOnlyCheck, allows to toggle state of the Fix selection to material |
| selectionButton_Callback.m | Callback to the handles.selectionButton_Callback, allows to add, subtract or replace selection |
| selectionClearBtn_Callback.m | Callback to the handles.selectionClearBtn, allows to clear the Selection layer |
| selectionDilateBtn_Callback.m | Callback to the handles.selectionDilateBtn, expands the selection layer |
| selectionErBtn_Callback.m | Callback to the handles.selectionErBtn, shrinks the selection layer |
| selectionFillBtn_Callback.m | Callback to the handles.selectionFillBtn, allows to fill holes for the Selection layer |
| seltypePopup_Callback.m | Callback to the handles.seltypePopup, allows to select tool for the segmentation |
| smoothImage_Callback.m | Callback to the smooth buttons and menus |
| toolbar_zoomBtn.m | Modifies magnification using the buttons in the toolbar of MIB |
| toolbarInterpolation.m | Function to set the state of the interpolation button in the toolbar |
| toolbarPlaneToggle.m | Callback to the change orientation buttons in the toolbar of MIB; it toggles viewing plane: xy, zx, or zy direction |
| toolbarResizingMethod.m | Function to set type of image interpolation for the visualization |
| unFocus.m | Move focus to the main window |
| update_drives.m | Updates list of available logical disk drives |
| update_filelist.m | Update List of files in the current directory |
| updateGuiWidgets.m | Update user interface widgets based on the properties of the opened dataset |
| updateMIB.m | UPDATEMIB MATLAB code for updateMIB.fig UPDATEMIB, by itself, creates a new UPDATEMIB or raises the existing singleton* |
| updateSegmentationLists.m | Update Segmetation Lists in the main window of im_browser.m |
| zoomEdit_Callback.m | Callback function for modification of the handles.zoomEdit |
| ImageFilters | |
| 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.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.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 |
| RandomForest | |
| MembraneDetection | |
| centeredRotate.m | |
| filterImageWithMembraneTemplateRotated.m | Filter image with a rotated template |
| filterSmallRegions.m | |
| gradientImg.m | |
| imsmooth.m | |
| makeColorOverlay.m | |
| membraneFeatures.m | Normalize image contrast |
| 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 | |
| uint8Img.m | |
| RF_Class_C | |
| 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 | |
| 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 |
| ib_MembraneDetection.m | Ib_MembraneDetection 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 |
| mib_Classifier.m | Mib_Classifier 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 |
| Supervoxels | |
| compile_c_files.m | Compile all c files |
| drawregionboundaries.m | |
| maskimage.m | |
| maxflow.m | |
| maxflow_v222.m | |
| anisodiff.m | ANISODIFF - Anisotropic diffusion |
| do_andiff_filtering.m | Filter dataset with anisotropic diffusion |
| do_andiff_filtering_backup.m | Filter dataset with anisotropic diffusion |
| do_diplib_andiff_filtering.m | Anisotropic diffusion filters from the Diplib library (http://www.diplib.org) |
| get_black_white_filter.m | Calculate black and white bitmap out of the image |
| getFrangiMask.m | Return Frangi mask generated from the img |
| getMorphMask.m | Return result of BW Morphological filters generated from the img |
| getStrelMask.m | Return Strel mask (imtophat/imbothat) generated from the img |
| ib_anisotropicDiffusion.m | Filter image with Anisotropic diffusion filters |
| ib_autoBrightness.m | Adjust brightness automatically |
| ib_contrastCLAHE.m | Do CLAHE Contrast-limited adaptive histogram equalization for the XY plane of the dataset for the currently shown or all slices |
| ib_contrastNormalizationMemoryOptimized.m | Normalize contrast between the layers of the dataset |
| ib_dilateSelection.m | Dilate (expand) the Selection layer in 2D or 3D |
| ib_doImageFiltering.m | Filter image with basic Matlab filters |
| ib_erodeSelection.m | Erode (shrink) the Selection layer in 2D or 3D |
| ib_fillMembranes.m | Fill holes between the slices for the same object |
| ib_imageMorphOpsGui.m | Ib_imageMorphOpsGui function is responsible for morphological operations done with images |
| ib_linearContrast.m | Linear Contrast adjustment for all or only shown image(s) |
| ib_MorphOpsGui.m | IB_MORPHOPSGUI MATLAB code for ib_MorphOpsGui.fig IB_MORPHOPSGUI, by itself, creates a new IB_MORPHOPSGUI or raises the existing singleton* |
| ib_removeBackground.m | Remove background of the image |
| ib_smoothImage.m | Smooth Mask, Selection or Model layer |
| ib_watershedGui.m | Ib_watershedGui function is responsible for watershed operations |
| ManGridBW.m | ManGridBW function allows to perform black and white thresholding of the image using the small blocks. In each of these blocks the image is thresholded with own coefficient |
| ImportExportTools | |
| 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 | |
| ib_exportToFiji.m | Export currently open dataset to Fiji |
| ib_fijiSelectDataset.m | Ib_fijiSelectDataset function is a dialog for selection of datasets from Fiji |
| ib_importFromFiji.m | Import dataset from Fiji to im_browser |
| ib_renderModelFiji.m | Render a model with Fiji engine |
| ib_renderVolumeWithFiji.m | Render 3D volume with Fiji |
| ib_runFijiMacro.m | Run command or macro on Fiji |
| ib_startMiji.m | Start Fiji |
| ib_stopMiji.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 |
| mib_saveHDF5Dlg.m | MIB_SAVEHDF5DLG MATLAB code for mib_saveHDF5Dlg.fig MIB_SAVEHDF5DLG, by itself, creates a new MIB_SAVEHDF5DLG 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 | |
| ib_getImarisDataset.m | Get a dataset opened in Imaris and corresponding meta-data |
| ib_getImarisDataset_standard_connection.m | Get a dataset opened in Imaris and corresponding meta-data |
| ib_renderModelImaris.m | Render a model in Imaris |
| ib_setImarisDataset.m | Send a dataset from MIB to Imaris |
| imaris_send_data_test.m | |
| SurfacesFromSegmentationImage.m | Old surface segmentation function written by Igor Beati from Bitplane |
| 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.m | |
| nrrdSaveWithMetadata.m | |
| Omero | |
| ib_importOmero.m | Ib_importOmero function is responsible for a dialog to advanced opening images from OMERO servers |
| ib_omeroLoginDlg.m | Varargout = ib_omeroLoginDlg(varargin) ib_omeroLoginDlg function is responsible for login to OMERO server |
| loadOmero_deploy.m | A modified version of loadOmero, with removed javaaddpath function |
| loadOmero_wrapper.m | A wrapper function to start Omero. Starts Omero in the Matlab and deployed versions of im_browser |
| amiraLabels2bitmap.m | Converts Amira Mesh Labels to bitmap matrix, for Amira ver. 5.2.2 |
| amiraMesh2bitmap.m | Converts Amira Mesh to bitmap matrix [1:height, 1:width, 1:colors, 1:no_stacks] |
| 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 |
| exportModelToImodModel.m | Export model to Imod model type |
| getAmiraMeshHeader.m | Get header of Amira Mesh file |
| getImageMetadata.m | Get metadata for images |
| getMRCfile.m | Read data in MRC/REC format |
| getMRCheader.m | Read header of MRC/REC file |
| ib_amiraImportGui.m | Ib_amiraImportGui function is responsible for a dialog to advanced opening of Amira Mesh files |
| ib_getImages.m | Generate image dataset from the files structure and the img_info containers.Map |
| ib_image2jpg.m | Save image in JPG format, 2D slices |
| ib_image2mrc.m | Export volume in MRC format |
| ib_image2png.m | Save image in PNG format, 2D slices |
| ib_image2tiff.m | Save image in TIF format, 2D slices or 3D stacks |
| ib_imwrite.m | Save image to a file using Matlab imwrite function |
| ib_loadImages.m | Load images from the list of files |
| ib_saveVideoGui.m | Ib_saveVideoGui function is responsible for saving video files of the datasets |
| ib_snapshotGui.m | Ib_snapshotGui function is responsible for making snapshots of the shown dataset |
| mib_chopDatasetGui.m | MIB_CHOPDATASETGUI MATLAB code for mib_chopDatasetGui.fig MIB_CHOPDATASETGUI, by itself, creates a new MIB_CHOPDATASETGUI or raises the existing singleton* |
| mib_rechopDatasetGui.m | MIB_RECHOPDATASETGUI MATLAB code for mib_rechopDatasetGui.fig MIB_RECHOPDATASETGUI, by itself, creates a new MIB_RECHOPDATASETGUI or raises the existing singleton* |
| parseStructToTree.m | Function to parse structure (XML) to uitree object based on struct2xml.m file by W. Falkena, ASTI, TUDelft, 27-08-2010 |
| stlwrite.m | STLWRITE Write STL file from patch or surface data |
| Misc_func | |
| imclipboard | |
| imclipboard.m | IMCLIPBOARD Copy and paste images to and from system clipboard |
| 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 |
| correlationAnalysis_script.m | Script to run correlation analysis for the Correlation Panel |
| extrema.m | |
| extrema2.m | Gets the extrema points from a surface |
| findjobj.m | |
| 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 |
| my_ginput.m | GINPUT Graphical input from mouse. [X,Y] = GINPUT(N) gets N points from the current axes and returns the X- and Y-coordinates in length N vectors X and Y. The cursor can be positioned using a mouse. Data points are entered by pressing a mouse button or any key on the keyboard except carriage return, which terminates the input before N points are entered |
| removeDotsFromFilePath.m | |
| rendertext.m | Render RGB text over RGB or grayscale images by Davide Di Gloria with the great contribution of Franz-Gerold Url |
| view3d.m | View3d Interactively rotate, zoom and pan the view of a 3-D plot |
| xlswrite2.m | XLSWRITE Stores numeric array or cell array in Excel workbook |
| Tools | |
| Align | |
| mib_calcShifts.m | Calculate alignment shifts between slices in I |
| mib_crossShiftStack.m | ImgOut = mib_crossShiftStack(imgIn, shiftsX, shiftsY, options) Shift stack provided in imgIn using translation numbers in shiftX and shiftY |
| mib_crossShiftStacks.m | [imgOut, bbShiftXY] = mib_crossShiftStacks(I1, I2, shiftX, shiftY) Shift I2 vs I1 using translation numbers in shiftX and shiftY |
| mib_DriftAlignDlg.m | MIB_DRIFTALIGNDLG M-file for mib_driftaligndlg.fig MIB_DRIFTALIGNDLG by itself, creates a new MIB_DRIFTALIGNDLG or raises the existing singleton* |
| windv.m | Windv(vector,window size) vectorized version of windv() smooths a vector using a window of +/- window size window size is reduced at the edges |
| AreaAnalysis | |
| cropObjectsDlg.m | CropObjectsDlg MATLAB code for cropObjectsDlg.fig cropObjectsDlg, by itself, creates a new cropObjectsDlg or raises the existing singleton* |
| ib_calcCurveLength.m | Calculate length of the curve objects in the slice |
| MaskStatsDlg.m | MaskStatsDlg is a GUI tool to generate statistics of 2D or 3D objects in the Model or Mask layers |
| mib_MaskStatsProps.m | MIB_MASKSTATSPROPS MATLAB code for mib_MaskStatsProps.fig MIB_MASKSTATSPROPS, by itself, creates a new MIB_MASKSTATSPROPS or raises the existing singleton* |
| regionprops3.m | Regionprops3 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 |
| RegionGrowing | |
| regiongrowing.m | REGIONGROWING A MEXed 2D/3D region growing algorithm |
| calc_correlation.m | Calculate correlation coefficients for img, script to run from Correlation panel of im_browser |
| generate_grid_block_size.m | Calculate size of the block to equally brake the image |
| ib_addText2Img.m | Add text label to the image |
| ib_calcCorrelation.m | Calculate correlation coefficients between frames in the XY plane |
| ib_calculatePixSizes.m | Recalculate pixel size (width, height) of the dataset to new units |
| ib_calculateResolution.m | Calculate image resolution in Inch as default for saving tifs |
| ib_connect_points.m | Connect points with search for a minimum gradients |
| ib_connectPoints.m | Generate a bitmap image with lines that connect points (pnts) |
| ib_flipDataset.m | Flip dataset horizontally, vertically or in the Z direction |
| ib_interpolateLines.m | Interpolate lines between the slices |
| ib_interpolateShapes.m | Interpolate the shapes between the slices |
| ib_invertImage.m | Invert image |
| ib_maskGenerator.m | Generate the Mask later |
| ib_renderModel.m | Render a model using isosurfaces |
| ib_rotateDataset.m | Rotate dataset in 90 or -90 degrees |
| ib_segmentation_3dBall.m | Do segmentation using the 3D ball tool |
| ib_segmentation_Annotation.m | Add text annotation to the dataset |
| ib_segmentation_Brush.m | Do segmentation using the brush tool |
| ib_segmentation_Lasso.m | Do segmentation using the lasso tool |
| ib_segmentation_MagicWand.m | Do segmentation using the Magic Wand tool |
| ib_segmentation_MembraneClickTraker.m | [output, handles] = ib_segmentation_MembraneClickTraker(yxzCoordinate, yx, modifier, handles) Trace membranes and draw a straight lines in 2d and 3d |
| ib_segmentation_ObjectPicker.m | Handles = ib_segmentation_ObjectPicker(yxzCoordinate, modifier, handles) Do a the targeted selection from Mask/Models layers |
| ib_segmentation_RegionGrowing.m | Do segmentation using the Region Growing method |
| ib_segmentation_SmartWatershed.m | Handles = ib_segmentation_SmartWatershed(modifier, handles) Do segmentation using the smart watershed. This function is a stripped version of the Watershed segmentation tool available from Menu->Tools->Watershed segmentation |
| ib_segmentation_Spot.m | Handles = ib_segmentation_Spot(y, x, modifier, handles) Do segmentation using the spot tool |
| ib_segmentBlackWhiteThreshold.m | Perform black and white thresholding for BW Threshold tool of the 'Segmentation panel' |
| ib_sizeExclusionFilter.m | Apply size exclusion filter on selection, model, or mask layers |
| ib_transposeDataset.m | Transpose dataset physically between dimensions |
| ib_updatePixSizeAndResolution.m | Calculate update resolution fields in the imageData.img_info(ImageDescription) or recalculate physical size of voxels |
| mark2selection.m | Place identification symbols to the selection layer |
| mib_compile_c_files.m | This script will compile all the C files % Compiling coherence filter |
| mib_resize3d.m | Resize 3D dataset |
| mib_stereologyGui.m | MIB_STEREOLOGYGUI MATLAB code for mib_stereologygui.fig MIB_STEREOLOGYGUI, by itself, creates a new MIB_STEREOLOGYGUI or raises the existing singleton* |
| im_browser.m | |
| im_browser_deploy.m | Try javaaddpath('c:', -end); catch err sprintf(s, err.identifier) end |
| im_browser_getDefaultParameters.m | Set default and stored from the previous session parameters of im_browser.m |
1.8.3.1 
