Microscopy Image Browser Release Notes for the beta development
Microscopy Image Browser Release Notes for the beta development
1.0000 (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
- Fixes
0.9990 (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
0.9980 (28.04.2015)
- 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 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
0.9970 (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
0.9960 (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
0.9950 (26.01.2015)
- Adaptation to Matlab R2014b
- Added Smart Watershed to the segmentation tools (Segmentation panel->Selection type->Smart watershed); check also improved watershed tool (Menu->Tools->Watershed)
- - Added number of morphological operations for images
- Menu->Image->Morphological operations 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
- 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 <ug_gui_menu_tools_watershed.html 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 <http://www.kaynig.de/demos.html Verena Kaynig> and <https://code.google.com/p/randomforest-matlab/ 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 <ug_panel_segm.html 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: 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
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
Alpha
Alpha version of Microscopy Image Browser was under development between 2010-2013.