Microscopy Image Browser Release Notes
Contents
- 1.233 07.10.2016
- 1.22 22.08.2016
- 1.21 29.06.2016
- 1.20 20.06.2016
- 1.10 07.04.2016 (update for 4D datasets)
- 1.02 20.01.2016
- 1.00 19.11.2015 Official Release
- 0.999 30.09.2015
- 0.998 05.05.2015
- 0.997 24.03.2015
- 0.996 06.03.2015
- 0.995 26.01.2015
- 0.9941 23.09.2014
- 0.9932 23.06.2014
- 0.9931 22.05.2014
- 0.9930 20.05.2014
- 0.9923 20.03.2014
- 0.9922 06.03.2014
- 0.9921 25.02.2014
- 0.9919 11.02.2014
- 0.9917 10.02.2014
- 0.9916 31.01.2014
- 0.9915 30.01.2014
- 0.9914 25.11.2013
- 0.9913 19.11.2013
- 0.9912 15.11.2013
- 0.9911 13.11.2013
- 0.9910 06.11.2013
- 0.9909 18.10.2013
- 0.9908 17.10.2013
- 0.9907 14.10.2013
- 0.9906 10.10.2013
- 0.9905 07.10.2013
- 0.9904 03.10.2013
- 0.9903 02.10.2013
- 0.9902 24.09.2013
- 0.9901 18.09.2013
1.233 07.10.2016
- Added convertion from uint16 to uint8 using the currently selected display adjustments settings (ver. 1.232)
- Completely rewritten alignment tool, now it is much faster and more reliable
- Added loading and combining MRC models from IMOD
- Added automatic scaling of scale bars for large snapshots
- Added adjustment of the image contrast during supervoxel calculation in the graphcut tool
- Added links to many short demo clips to the Help (ver. 1.233)
- Improved performance of the shape interpolation tool (ver. 1.232)
- Update movie rendering, now it will also render movies from 16-bit images
- Update of the alignment tool for the YZ and XZ dimensions (ver. 1.233)
- Fix of uncleared memory after closing of datesets, introduced in MIB 1.20
- Few small fixes in the mib_measureTool and in the alignment tool (ver. 1.231)
- The 'handles' handle has been removed from getImageMetadata(filenames, options); the required fields handles.matlabVersion and handles.preferences.Font were included into the options structure
1.22 22.08.2016
- Added extra options for exporting models and masks from the Statistics window
- Mostly bug fixes
1.21 29.06.2016
- Fixed horizontal/vertical flipping for 2D datasets
- Fix of several small bugs
1.20 20.06.2016
- Added Volume Rendering for small datasets (Toolbar->Volume rendering button)
- Added the Crop To mode to the Crop tool (Menu->Dataset->Crop dataset...)
- Added split color channels mode for the snapshots
- Added possibility to copy ROI areas to the Selection layer (ROI Panel->the ROI to Selection button)
- Added rotation of a single color channel for square-shaped images (Menu->Image->Color channels->Rotate channel...)
- Updated Image Description dialog: Path Panel->Info
- Updated the Chop/Rechop modes
- Updated Bio-Formats library to 5.1.10
- Fixed version check for MacOS Matlab R2012a
- Fixed a bug during object unselection in the Object picker tool
- Bug fixes
- java_path.txt was renamed to mib_java_path.txt and placed to the first folder on the search path (usually [username]\Documents\MATLAB; path to this file will be displayed in the command prompt during start of MIB)
1.10 07.04.2016 (update for 4D datasets)
- Modification of MIB to work with 4D data (H,W,C,Z,T)
- Replaced imageData.slices(1:4,:) matrix variable with a cell imageData.slices{1:5}(:)
- Replaced imageData.slicesColor variable with imageData.slices{3}(:)
- Renamed functions: getData3D->getData2D; getData4D->getData3D; getData5D->getData4D; setData3D->setData2D; setData4D->setData3D; setData5D->setData4D;
- Added ib_getStack, ib_setStack methods for working with individual stacks of 4D datasets
- Added flip time points of the dataset (Menu->Dataset->Transform->Flip T)
- Added transpose of Z to T dimension (Menu->Dataset->Transform->Transpose Z<->T)
- Added insert of an empty color channel to the dataset (Menu->Image->Color channels->Insert empty channel)
- Added possibility to delete a time frames (Menu->Dataset->Delete slice->Delete frame(s)...)
- Added additional modes for CLAHE contrast (Menu->Image->Contrast->CLAHE)
- Added Bin2, Bin4, Bin8 buttons to the Snapshot dialog
- Added the link checkbox to the Display adjustment dialog to link modification of settings for all shown color channels
- Added Frangi 2D/3D filters to the Image Filters panel, the panel was also redesigned
- Added t-parameter to imageData.clearSelection
- Added reading/writing of BigDataViewer HDF5 format for Fiji
- Improved data exchange with Imaris, added export of models as volumes to Imaris (Menu->Models->Export model to...->Imaris as volume)
- Improved loading and saving of HDF5 datasets
- Improved performance of many manual segmentation tools
- Modified call of ib_moveLayers
- Updated TIF reader to accept pyramidal TIFs from Zeiss microscopes
- Updated Menu->Image->Invert image with various options
- Updated programming tutorials
- Optimized Undo functionality to make it faster and use less memory
- Bug fixes
1.02 20.01.2016
- Added resizing of panels
- Added undo for the brush in the superpixel mode (press Ctrl+Z while drawing to unselect superpixels)
- Added save models using the STL format (Menu->Models->Save model as...)
- Added a button to change image interpolation type to the toolbar (nearest/bicubic) and removed bilinear interpolation from the visualization options
- Updated the drawing of scalebars, now they are displayed as round numbers
- Updated the Watershed/Graphcut segmentation tool
- Fixed the length of a scale bar in snapshots after resizing
- Fixed elements of GUI that were not properly resized
- Fixed use of the memory function for non-windows operating systems
1.00 19.11.2015 Official Release
- Added X/Y calibration of the loaded dataset using an existing scale bar printed on images (Menu->Dataset->Scale bar)
- Replaced function that calculates adjacency of supervoxels in the graphcut and classifier tools to Region Adjacency Graph (RAG) by David Legland
- Added Stereology mode to count intersections of materials of the model with a grid lines (Menu->Tools->Stereology)
- Added watershed superpixels and supervoxels to the graphcut segmentation
- Added watershed superpixels to the Brush tool
- Added watershed superpixels/supervoxels to the superpixel classifier
- Added customization dialog for key shortcuts (File->Preference->Shortcuts)
- Added detection of LUTs for color channels when using the Bio-Formats reader
- Fixes
0.999 30.09.2015
- Added Maxflow/mincut semi-automatic segmentation (Menu->Tools->Watershed/Graphcut segmentation)
- Added Supervoxel/superpixel based classifier (Menu->Tools->Classifiers->Supervoxels classification)
- Added a mode for chopping and combining back large images (Menu->File->Chop images...)
- Added possibility to calculate multiple properties of objects in the Get Statistics... dialog (Menu->Models->Model Statistics...)
- Added rendering of measurements to snapshots
- Added modification of the adaptive coefficient for the brush with the supervoxels mode: while drawing use the mouse wheel to change the coefficient
- Added Undo for the Brush tool with superpixels, while selecting superpixels press the Ctrl+Z shortcut to undo selection of the last superpixel
- Added RegionGrowing mode to the Magic Wand tool
- Added Affine Transformation mode to the Alignment tool
- Added new methods to access the dataset: imageData.getData2D, imageData.getData3D, imageData.getData4D, imageData.setData2D, imageData.setData3D, imageData.setData4D that replace old methods imageData.getDataset and imageData.setDataset
- Added possibility to crop dataset based on detected 2D objects: Menu->Model Statistics...->Run->Select objects and press the right mouse button->Crop to a file/matlab...
- Modified syntax of the imageData.getDatasetDimensions method call
- Modified Make video dialog: now it is not modal; added back-and-forth option
- Preserve the current magnification during the orientation switch using the Alt+1, Alt+2 and Alt+3 shortcuts
0.998 05.05.2015
- Added stand-alone version for Mac OS (tested with OS X Yosemite, ver. 10.10.3 and Matlab R2014b)
- Added Measure Tool (Menu->Tools->Measure length->Measure tool)
- Added superpixels mode for the brush tool
- Added possibility to crop dataset based on detected 3D objects: Menu->Model Statistics...->Run->Select objects and press the right mouse button->Crop to a file/matlab...
- Completely rewritten roiRegion class to perform faster in the R2014b and later
- Added possibility to change font name in the Menu->File->Preferences dialog
- Fixed many issues with Linux and MacOS compatibility
0.997 24.03.2015
- Added highlighting of the current file, when switching the buffers
- Added names of series during opening of datasets using Bioformats
- Added morphological filters to the Mask Generators panel: imextendedmax, imextendedmin, imregionalmax, imregionalmin
- Added a context menu to the Pixel Information text of the Path panel for instant jump to desired position within the dataset
- Added a new dialog to define coordinates of the bounding box
- Update: colors of materials are stored with the ImageData class, now the colors are also saved together with the model
- Update: the LUT colors are stored in the imageData class
- Update: Bio-formats library is now bioformats_package.jar
- Update: Connection to Imaris
- Modified the Mask Generators panel
- Fixed opening of images with different XY and color channels using Bioformats
- Fixed generation of JPG snapshots for 16-bit images
- Fixed triggering of the key press callback during the pan mode
- Fixed dublicates of the brush cursor in some situations
0.996 06.03.2015
- Added CZI format to the list of extensions
- Added a custom input dialog
- Annotations and measure tools are available when the model/selection layers are turned off
- Updated to the new server for updates, at http://mib.helsinki.fi
- Multiple fixes in the mode when the model/selection layers are turned off
- Bug fixes
0.995 26.01.2015
- Adaptation to Matlab R2014b
- Added Smart Watershed to the segmentation tools (Segmentation panel->Selection type->Smart watershed); see also improved watershed tool
- Added number of morphological operations for images: Menu->Image->Morphological operations
- Added increase of the brush size by ~40% when starting the Erase mode (by holding the Control key)
- Added import/export images from Imaris : Menu->File->Import(Export)->Imaris (requires Imaris and ImarisXT)
- Added import images from URL link: Menu->File->Import->URL
- Added Annotations to the statistical filtering window. The right mouse button above the Statistics table starts a popup menu with access to annotations.
- Added Gradient 2D and Gradient 3D filters to the Image Filters panel
- Added tools for manipulation with the colormaps in the Preferences dialog
- Added rendering models with Imaris: Menu->Models->Render model...->Imaris
- Added calculation of the following properties for 3D objects: MajorAxisLength, SecondMajorAxisLength, MinorAxisLength, MeriodionalEccentricity, EquatorialEccentricity
- Added Zoom in/out using the Alt+Mouse wheel combination
- Many functions moved from im_browser.m to a separate files located in the GuiTools directory
- Improved rendering of large images using the 'nearest' resampling mode
- Updated and significantly improved the watershed tool
- Renamed the Mask/Model segmentation tool to Object Picker
- Fixed import of models with more colors than defined in MIB
- Fixed rotation of datasets with the Mask or Model layers
- Moved Top and Bottom hat filters to the morphological operations for images: Menu->Image->Morphological operations
0.9941 23.09.2014
- Added color palettes for materials of models, Menu->File->Preferences->Colors
- Added conversion to HSV colorspace, test version
- Added possibility to plot a histogram in the Statistics dialog
- Added restore default settings button to the Preferences window
- Added paste from Clipboard: Menu->File->Import image from->Clipboard
- Rearranged files/directories
- Updated BioFormats reader
- Fixed bugs with dynamic sliders in the deployed version
- Fixed bug in the wrong shifts of datasets during alignmen
- Fixed bug with ROI during duplication of datasets
0.9932 23.06.2014
- Added the Random forest classifier for tests, original functions from Verena Kaynig and randomforest-matlab by Abhishek Jaiantilal.
- Added EndPointsLength statistics for 3D lines
- Updated EndPointsLength statistics is now reported in the image units
- Updated the Make Snapshot dialog
- Updated the Image Adjustment dialog
- Updated the Magic Wand tool: it is possible to specify an effective radius of for the tool
- Updated the Spot tool: much faster
- Fixed MembraneClickTracker tool for straight lines in 3D with width = 1 and for the points at the edge of the image
- Fixed saving of individual materials of the models
0.9931 22.05.2014
- Added: conversion of multichannel images to greyscale
- Improved: refreshing of the opened auxiliary windows
- Updated: the watershed segmentation was updated to seeded watershed.
- Fixed: image rescaling during resize of the main window
0.9930 20.05.2014
- Added a layer for Annotations, a label that may be placed at desired part of the dataset (Segmentation panel->Selection type->Annotations).
- Improved speed of image generation when the Show model switch is On
- Some sliders were updated to allow real-time feedback
- Modified the Segmentation panel by introducing the Show all checkbox
- Added possibility to synchronize the views between opened datasets. Use a popup menu for the buffer buttons in the Directory contents panel.
- Added indication of intensity of the 4th color channel during the mouse move above the image
- Added Rectangle, Ellipse and Polyline type of selections to the Lasso segmentation tool
- Added possibility to use original filenames when saving dataset in Jpeg, PNG and TIF formats
- Added possibility to see a single channel using a Ctrl+left mouse click above the checkboxes of the Colors table in the View settings panel.
- Added sorting by slice number to the Get Statistics dialog (right mouse click above the Sort button)
- Updated the Adjust Display dialog with colors and right mouse callbacks for the sliders to set sliders to 0 and maximal possible values
- Improved BioFormats reading dialog
- Fixed saving models (removed the Selection and Mask layers) using the Save Model button in the toolbar
- Fixed generation of statistics for the currently shown slice
0.9923 20.03.2014
- Changed implementation of the Membrane Click Tracker tool. Now Shift+mouse click defines the first point of the membrane domain.
- Fixed very long parameter names in the Dataset Info window; added display in the upper part of the Dataset Info window to show entry in the selected cell.
- The Image Profile functions were updated for multicolored datasets
0.9922 06.03.2014
- Added the Interpolation type button to the toolbar.
- Added possibility to insert another dataset to the opened dataset.
- Skip dataset selection for BioFormats reader, when only one dataset present
- Extended filename information of the current dataset in the View Image Panel
- Several bug fixes and improvements
0.9921 25.02.2014
- Added watershed segmentation, Menu->Tools->Watershed
- Added support for NRRD format, a native format of 3D slicer
- Added file name to the title of the Image View panel
- Added landmark alignment mode for the opened datasets, some fixes of the alignment.
- Renamed Menu->Measure to Menu->Tools
- Modified formation of Z stacks with datasets of different dimensions, now the data is not cropped.
- The brightness slider in the View settings panel was replaced with the live stretch check box. When enabled im_browser automatically adjust contrast for each shown image; but only for preview, the actual image intensities will not be affected.
- Fixed auto-updater for Matlab release R2012a and older.
- Fixed Delete Slice for multiple slices
0.9919 11.02.2014
- Added posibility to define a step for thresholding sliders in the BW thresholding selection tool, available via a popup menu (right mouse click on the sliders)
- Fixed import models bug
- Set the Column Format in the Value column of the MaskStatsDlg to the 'short g' representation.
0.9917 10.02.2014
- Added possibility to change font size
- Added a context menu to the Adjust channel button of the Display adjustment dialog. The menu allows contrast adjustment of the currenly shown slice.
- Updated selection of the fast-access tools for the "D" key shortcut. Now the tools can be selected using the D checkbox in the Segmentation panel
0.9916 31.01.2014
- Improved brush performance for the brush size
0.9915 30.01.2014
- Added Matlab normalized 2-D cross-correlation to the Alignment options for tests
- It is possible to open multiple series using BioFormats reader
- Updated Stop Fiji routine
- Improved sensitivity of the Membrane ClickTracker tool
- Fixed network update for the deployed version
- Fixed background colors in some windows
0.9914 25.11.2013
- Large update of the ROI mode. Now the ROIs are bound to the image dataset, so it is possible to have set of ROI for each opened image
- Added positioning of the logList window to the bottom of the main window
- Fixed ib_maskGenerator.m for multi-colored datasets
- Fixed implementation of BioFormats for the deployed version
0.9913 19.11.2013
- Added store position of the selected mode in the Get Statistics dialog, plus some other modifications in the same dialog
- Fixed a bug in the imageData.plotImage function, when the brightness slider is used
- Added delete the maskStatsDlg and ib_datasetInfoGui dialogs after close of im_browser
0.9912 15.11.2013
- Added Duplicate dataset to the context menu of the buffer buttons: Directory Contents->Buffer buttons->right mouse click->Duplicate dataset
- Added 'Enter' and 'Esc' shortcuts to Load Bioformats, make snapshot, make movie, morph ops dialogs
- Added synchronozation of Image Info tables between different datasets, using FindJObj.m function
- Moved all functions from ImageData class to own files
- Updated coloring of the brush tool during the brush motion for 16bit images
0.9911 13.11.2013
- Added a new window for showing parameters of the dataset (Path panel->Info button)
- Added ROI mode to the Make snapshot dialog (Menu->File->Make Snapshot...)
- Added ROI mode to the Make video dialog (Menu->File->Make Movie...)
- Added use of system TEMP folder to store im_browser parameters as a second choice, when c:\temp is not available for writing (settings are stored in im_browser.mat)
- Added PNG format to Save image as dialog
- the Adjust Display window does not show histogram for modified gamma, but shows histogram for all color channels
- Combine as color channels - added to the popup menu in the file listing of the Directory contents panel
- Updated saving of multichannel images in Amira Mesh format
- Updated the color table in the View settings panel
- Replaced '\t' character in the ImageDescription field to the '|'
0.9910 06.11.2013
- Added short release notes in the automatic update
- Added LUT (look-up table) for defining a custom set of colors for color channels
- Added copy color channel: Menu->Image->Color Channels->Copy channel...
- Added copy color channel: Menu->Image->Color Channels->Invert channel...
- Updated Preferences dialog: Menu->File->Preferences
- Moved some functions from the class to external files
- Renamed cropImage to cropDataset function in the imageData class
0.9909 18.10.2013
- Added tooltips to some toolbar buttons
- Added rehash of files after using web-update of im_browser
- Added TIF to bio-formats file filter
- Added synchronization of the Material list boxes in the segmentation panel (Materials List->right mouse button->Sync all lists)
- Updated un-focusing behavior with some edit and combo boxes
- Updated colors of the Preferences dialog;
- Fixed import/export img_info containers.Map class object with description of the dataset. The img_info map is a handle so it has to be reinitialized: img_info_new = containers.Map(keys(img_info), values(img_info));
0.9908 17.10.2013
- Added preservation of the bounding box during alignment of stacks
- Fixed bug of the bounding box settings (introduced in 0.9904)
- Minor improvements
0.9907 14.10.2013
- Fixed resizing of the slider responsible for change of slices
0.9906 10.10.2013
- Added 3D Frangi filter (Mask Generators->Frangi filter)
0.9905 07.10.2013
- Added selection of the first and last points for rendering videos (Menu->File->Save as video...)
0.9904 03.10.2013
- Taken into account stage rotation bias when calculating the bounding box (rotation stage bias field in the Menu->Dataset->Bounding Box dialog).
0.9903 02.10.2013
- Fixed the memory clearance after disabling of the Selection mode in the preference dialog for the uint6 models
0.9902 24.09.2013
- Added fast pan mode, for fast navigation when showing large XY images (Toolbar->Fast pan mode)
- Fixed in the Menu->Selection->Mask and Mask->Selection
0.9901 18.09.2013
- Added ultimate erosion
- Implementated automatic check for updates
- Fixed modification of ROI for large images
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