The 3D Visualization Figures and GUI Data Generation

CMap Paper Preprint:

Quantitative cell morphology in C. elegans embryos reveals regulations of cell volume asymmetry

November 2023

DOI: 10.1101/2023.11.20.567849

LicenseCC BY-NC-ND 4.0

Generation of 3D GUI Data in ITK-SNAP-CVE of CMap paper

Cell-wise GUI Data

• generate_gui_data_cmap.py (for 8+4 uncompressed embryos in CMap database)
• generate_gui_data_cshaper.py (for 17 compressed embryos in CShaper database)

Fate-wise GUI Data

• generate_fate_cell_cmap.py (for 8+4 uncompressed embryos in CMap database)
• generate_fate_cell_cshaper.py (for 17 compressed embryos in CShaper database)

Generation of 3D Illustration Figures in CMap Paper

Generation of Rendering .obj Files for Blender

See the details and readme.md in Github (biomedical-tools).

Useless Notes

CMap Visualization Code

Steps

1. generate segmentation
2. calculate the wrong division cells in FILE test_post_segmentation.py of PROJECT CellShapeAnalysis.
3. re-assign the label in FILE test_post_segmentation.py of PROJECT CellShapeAnalysis with frozen tem data.
4. re-calculate the statistical data of CMap in def update_wrong_dividing_cell_stat_CMap() in FILE test_post_segmentation.py of PROJECT CellShapeAnalysis.
5. assemble them in the FILE data_repair_stat_code.py of PROJECT MembraneProjectCode with resolution 0.18.
6. generate gui in PROJECT MembraneProjectCode with only order gui=true in FILE TRAIN_TEST.yaml
7. run FILE repair_Stat.py in PROJECT GUIData to ensure the contact display in CVE software is normal.

CShaper Visualization Code

Steps

1. generate segmentation
2. collect materials
3. generate the volume, surface area, contact surface area in PROJECT CellShapeAnalysis
4. generate *Stat.csv,*volume.csv,*surface.csv, in file cshaper_data_repaircode.py of PROJECT MembraneProjectCode
5. generate GUI data in this project, the 0.25**2 and **3 coefficient will applied to the data here
6. run FILE repair_Stat.py in PROJECT GUIData to ensure the contact display in CVE software is normal.

Path

1. raw membrane data (raw_data_folder=r'D:\MembraneProjectData\GUIData\WebData_cshaper_v1' or D:\cell_shape_quantification\DATA\Segmentation Results\RawData)