analysis

Analysis

This folder contain plotting code for Figures in the paper. Some scripts require Napari to run: pip install "napari[all]".

You can also run these notebooks with:

• Apptainer: apptainer exec --nv <path/to/mousechd.sif> jupyter-notebook (using -B to mount data if necessary)
• Docker:
  • sudo docker run --gpus all -v <path/on/host>:</path/on/image> -it -p 8888:8888 hoanguyen93/mousechd
  • Inside the container: jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root

Main figures

Figure 1

• Figure 1a: see scripts/09_analyze.sh

  • Plot 3D stages: mousechd viz3d_stages -h to see the instruction. Example:

    mousechd viz3d_stages \
    -imdir "$PROCESSDIR/Imagine/images" \
    -maskdir "$PROCESSDIR/Imagine/heart-masks" \
    -stage "E18.5" \
    -imname "NH_1045" \
    -savedir "$SAVEDIR/Fig01" \
    -suffix "bbx" \
    -bbx "both" \
    -zoom 2.8 \
    -cam_angles "(0,30,15)" \
    -crop 0

  • Plot 2D stages: mousechd viz_stacks -h to see the instruction. Example

    -impath "$PROCESSDIR/Imagine/images/NH_221c" \
    -crop "axial" \
    -annotate 1 \
    -maskpath "$PROCESSDIR/Imagine/heart-masks/NH_221c" \
    -pad "(1,1,1)" \
    -num 5 \
    -trans_val 30 \
    -savedir "$SAVEDIR/Fig01" \
    -plot_zline 1 \
    -zline_color 'b' \
    -plot_border 1 \
    -color 'b'
    

• Figure 1b & 1c: See 01_eda.ipynb

Figure 3

• See 02_segmentation.ipynb

Figure 4

• See 03_diagnosis.ipynb

Figure 5

• Figure 5a: scripts/09_analyze.sh
• Figure 5b-g: 03_diagnosis.ipynb

Supplementary figures

Supplementary Figure 1

• See 02_segmentation.ipynb

Supplementary Figure 3

• See 03_diagnosis.ipynb

Supplementary Figure 4

• See 01_eda.ipynb

Supplementary Figure 5

• See scripts/08_explain.sh

Revision

Improve plots from the feedback of reviewers. See 04.revision.ipynb for more details:

• Improve the readability of Venn diagrams