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
- 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)
- 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)
See the details and readme.md in Github (biomedical-tools).
- generate segmentation
- calculate the wrong division cells in FILE test_post_segmentation.py of PROJECT CellShapeAnalysis.
- re-assign the label in FILE test_post_segmentation.py of PROJECT CellShapeAnalysis with frozen tem data.
- re-calculate the statistical data of CMap in def update_wrong_dividing_cell_stat_CMap() in FILE test_post_segmentation.py of PROJECT CellShapeAnalysis.
- assemble them in the FILE data_repair_stat_code.py of PROJECT MembraneProjectCode with resolution 0.18.
- generate gui in PROJECT MembraneProjectCode with only order gui=true in FILE TRAIN_TEST.yaml
- run FILE repair_Stat.py in PROJECT GUIData to ensure the contact display in CVE software is normal.
- generate segmentation
- collect materials
- generate the volume, surface area, contact surface area in PROJECT CellShapeAnalysis
- generate *Stat.csv,*volume.csv,*surface.csv, in file cshaper_data_repaircode.py of PROJECT MembraneProjectCode
- generate GUI data in this project, the 0.25**2 and **3 coefficient will applied to the data here
- run FILE repair_Stat.py in PROJECT GUIData to ensure the contact display in CVE software is normal.
- raw membrane data (raw_data_folder=r'D:\MembraneProjectData\GUIData\WebData_cshaper_v1' or D:\cell_shape_quantification\DATA\Segmentation Results\RawData)