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    Version 1.00 19.11.2015
  • 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
  • minor fixes

    Version 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.getData3D, imageData.getData4D, imageData.getData5D, imageData.setData3D, imageData.setData4D, imageData.setData5D 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

    Version 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 the 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

    Version 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

    Version 0.996 06.03.2015
  • Adaptation to Matlab R2014b
  • 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

    Version 0.995 14.01.2015
  • 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

    Version 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 alignment
  • Fixed bug with ROI during duplication of datasets

    Version 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

    Version 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

    Version 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

    Version 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

    Version 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

    Version 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

    Version 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

    Version 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

    Version 0.9916 31.01.2014
  • Improved brush performance for the brush size

    Version 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

    Version 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

    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

    Version 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

    Version 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 '|'

    Version 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

    Version 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))

    Version 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

    Version 0.9907 14.10.2013
  • Fixed resizing of the slider responsible for change of slices

    Version 0.9906 10.10.2013
  • Added 3D Frangi filter (Mask Generators->Frangi filter)

    Version 0.9905 07.10.2013
  • Added selection of the first and last points for rendering videos (Menu->File->Save as video...)

    Version 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)

    Version 0.9903 02.10.2013
  • Fixed the memory clearance after disabling of the Selection mode in the preference dialog for the uint6 models

    Version 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

    Version 0.9901 18.09.2013
  • Added ultimate erosion
  • Implementated automatic check for updates
  • Fixed modification of ROI for large images

List of changes during early-beta is not available



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