Metadata-Version: 2.1
Name: brainseg
Version: 0.0.5
Summary: A brain segmentation tool
Home-page: https://github.com/alleetw101/brainseg
Author: Alan Lee
Author-email: alleetw101@gmail.com
License: UNKNOWN
Description: # Brain Seg
        
        ![Segmentation Comparison](assets/SegmentationComparison.jpg)
        
        A brain segmentation tool using machine learning
        
        Under development
        
        This software has NOT been approved for medical analysis/diagnosis. Please use other
        approved software for medical use.
        
        # Models
        SavedModels for use can be found at [Google Drive](https://drive.google.com/drive/folders/1DuKPhzKcxWUNXYxYbSNw8zydiAG7a8qw?usp=sharing).
        
        Models were trained using the Mindboggle-101 data:
        
        Klein, Arno, 2016, "Mindboggle-101 manually labeled individual brains", 
        https://doi.org/10.7910/DVN/HMQKCK, Harvard Dataverse, V2
        
        A Klein, SS Ghosh, FS Bao, J Giard, Y Hame, E Stavsky, N Lee, B Rossa, M Reuter, EC Neto, A Keshavan. 2017. 
        Mindboggling morphometry of human brains. 
        PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 
        (bioRxiv 2016 preprint)
        
        # Options
            positional arguments:
              filepath              Path of file to segment
            
            optional arguments:
              -h, --help            show this help message and exit
              -s SEGMENT, --segment Segments using provided SavedModel (Directory path required)
              --segment-precision   Float32 or float64 {32,64}
              --output OUTPUT, -o   Output filepath
              --output-channels     Number of channel in output image {1,3}
        
        
        # Usage Examples
        ```bash
        # Segments a sample nifti scan
        $ brainseg sample.nii.gz -s sampleSavedModel -o output.nii.gz
        ```
        
        # Model Training Graphs
        
        SavedModel_210303
        ![accuracy_210303](assets/accuracy_210303_235240.png)
        ![loss_210303](assets/loss_210303_235240.png)
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
