MITK v2023.04

Updated 268 Days AgoPublic

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News for MITK Workbench users

For MITK v2023.04, we focused mainly on segmentation again and we are already excited about your feedback on many improvements, features and a further streamlined segmentation workflow.

Segmentation

TotalSegmentator AI segmentation tool

We introduced a segmentation tool based on the popular TotalSegmentator, a fully automatic AI-based segmentation of 104 classes in CT images.

Install and set up TotalSegmentator from within the MITK Workbench with only a few clicks to perform fully automatic segmentations of your CT images.

The MITK Workbench even allows you to apply TotalSegmentator for all time steps of dynamic 4-d CT images.

See the user guide for more details on the TotalSegmentator AI segmentation tool.

Example: 4-d heart segmentation done with TotalSegmentator in the MITK Workbench

New label management

Up until now we organized labels of multi-label segmentations in layers, which allowed you to have overlapping labels in a single segmentation image. However, switching between layers was a bit clunky from time to time.

We completely reworked and optimized the Segmentation plugin to now have everything at sight at once, so you can easily switch between labels of different layers, which are now called groups.

See the user guide for more details on groups and labels.

Instance segmentation

You now can have multiple instances of the same label to better facilitate the segmentation of distriubted entities like metastases or other pathological sites.

See the user guide for more details on label instances.

MxN Display/Editor

In addition to the default 4-window-display, we have introduced a customizable display that can be adapted to your needs. You can change the amount of windows, their view directions, and even which data is shown in each individual window. Windows can be synchronized with each other to show the same data, or set to show an individual selection. Similarly, you can navigate through each window individually, or synchronize their movement to e.g. scroll through all windows at once. After you have created a certain window layout, you can save it and load it again later.

See the user guide for more details on the MxN Display/Editor.

VP9/WebM support in Movie Maker

You can now choose your preferred video output format in the Preferences (Ctrl+P) for videos recorded with the Movie Maker plugin:

• VP9 (*.webm): Open, royalty-free, highly efficient and modern video codec.
• H.264 (*.mp4): The de-facto standard for video in the web for many years. Use for higher compatibility with old devices or software.

High DPI support

The MITK Workbench now works fine with multi-monitor setups that have different DPI settings and scale its user interface more appropriately at high DPI settings.

💔 Known issues

• The Live Wire and Lasso segmentation tools may cause trouble in free-draw mode when drawing beyond image boundaries.
• While the segmentation interpolation now works also with multi-label segmentations, it is currently not considered to be completely robust against all edge cases. Use carefully and consider to save your project beforehand.

News for developers

While we didn't touch any of our third-party dependencies this time, we have a few API-breaking changes that may affect you.

Segmentation

The revamp of the Segmentation View is based on a transition from the legacy LabelSetImage class towards a more flexible and easier to use MultiLabelSegmentation class. The transition is not yet finished but will be accompanied by an extensive migration guide soon.

Please contact us if you need to adapt earlier.

Note that we had to make changes to our NRRD based MITK Segmentation file format. We provide a unit-tested legacy file reader, though. You should not get into any trouble in that regard.

Preferences

Preferences moved completely from BlueBerry to the MitkCore as core service and hence are now accessible from modules as well. The migration is straight forward as we kept the public API as similar as possible.

See the migration guide for more details.

🔥 Disclaimer for API-breaking changes

We discontinued the extensive listing of API-breaking changes as the vast majority of them are straight forward to resolve or do not affect the absolute majority of developers at all. The ratio between the time and effort spent for writing these reports and actual developer feedback turned out to be greatly imbalanced.

Complex or critical API changes will still be accompanied by migration guides.

In case you experience any trouble while migrating to the newest version of MITK, please do not hesitate to contact us.

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