mousechd 0.0.1a4

Segmenting hearts and screening congenital heart diseases in mice

Screening of Congenital Heart Diseases (CHD) in mice with 3D CTscans.

Napari Plugin: MouseCHD Napari plugin

Installation:

• Create virtual environment: conda create -n mousechd python=3.9
• Activate the environment: conda activate mousechd
• Install the package: pip install mousechd

How to use

This For user-friendly interface, refer to MouseCHD Napari plugin in this repository: https://github.com/hnguyentt/mousechd-napari

Raw data structure

It is recommended that your data is structured in the following way:

    DATABASE # your database name
    └── raw # raw folder to store raw data
        ├── NameOfDataset1 # name of dataset
        │   ├── images_20200206 # folder to store images recieved on 20200206 [YYYYMMDD]
        │   ├── masks_20210115 # folder to store masks recieved on 20210115 [YYYYMMDD]
        │   ├── masks_20210708 # folder to store masks recieved on 20210708 [YYYYMMDD]
        │   └── metadata_20210703.csv # metadata file received on 20210703 [YYYYMMDD]
        └── NameOfDataset2 # name of another dataset
            └── images_20201010
            ......

Preprocessing

This step standardizes the data into the same spacing and view. Note: although this script supports different file formats, we recommend using NIFFTI format as it contains information about the spacing and orientation of the image.

mousechd preprocess.py \
    -database <PATH/TO/DATABASE> \
    -maskdir <PATH/TO/MASK/DIR> \ # relative to database
    -masktype NIFFTI \ # relative to database
    -metafile <PATH/TO/META/FILE> \
    -outdir <PATH/TO/OUTPUT/DIR>

Heart segmentation

• Preparing data for training and testing nnUNet:

  mousechd segment -indir [INPUT/DIRECTORY] -outdir [OUTPUT/DIRECTORY]
  

• Post-process nnUNet

mousechd postprocess_nnUNet \
    -indir <PATH/TO/SEGMENTATION/BY/nnUNet> \
    -outdir <PATH/TO/OUTDIR>

CHD detection

Analysis

For some visualizations (), [Napari] is required. To install: conda install -c conda-forge napari A detailed analysis of the results can be found in the folder analysis.

Acknowledgements

• INCEPTION funding: INCEPTION