This folder contain plotting code for Figures in the paper. Some scripts require Napari to run: pip install "napari[all]"
.
-
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 5a: scripts/09_analyze.sh
- Figure 5b-g: 03_diagnosis.ipynb
- See 01_eda.ipynb
Improve plots from the feedback of reviewers. See 04.revision.ipynb for more details:
- Improve the readability of Venn diagrams