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MONAI based image augmentator
Key Investigators
- Ciro Benito, Raggio (Karlsruhe Institute of Technology, Germany)
- Paolo, Zaffino (Magna Graecia University of Catanzaro, Italy)
- Maria Francesca, Spadea (Karlsruhe Institute of Technology, Germany)
Presenter location: In-person
Project Description
MONAI and PyTorch based medical image augmentation tool that can be integrated in Slicer.
The project aims to be a low-code version of the tool: https://github.com/ciroraggio/AugmentedDataLoader.
It’s designed to operate on a dataset of medical images and apply a series of specific transformations to each image. This process augments the original dataset, providing a greater variety of samples for training deep learning models.
Objective
- Creating an intuitive graphic interface for the module
- Parallelising the augmentation process to optimally utilise resources
Approach and Plan
- Create the extension
- Implement the augmentation process
- Try to parallelise the process so that it takes as little time as possible on large data sets
Progress and Next Steps
- Implemented graphic interface for loading images and masks, choosing transformations and saving images.
- Implemented and tested MONAI spatial transformations such as Rotation, RandRotation, Flip, Resize.
- Partially implemented input validation and MONAI intensity transformations, it will be completed in the future.
- Partially implemented “Preview” feature, which allows the output of transformations to be viewed directly in the scene before saving them in the OS, will be completed in the future.
Illustrations
![filled](https://github.com/NA-MIC/ProjectWeek/assets/96300975/cc595232-fb44-4ff3-84eb-4a5ef52ec10c)
Files are saved as follows:
![output_folder](https://github.com/NA-MIC/ProjectWeek/assets/96300975/f69f0408-d680-4e60-8675-dfac3e0ac5ed)
Example of image after transformation in the scene:
![output_scene](https://github.com/NA-MIC/ProjectWeek/assets/96300975/4a06470e-8a1a-4b6b-87ed-82913aecc528)
Background and References
GitHub Project: https://github.com/ciroraggio/SlicerAugmentator