Ascidian package

Contents

• 1. Release notes
  • 1.1. Developer version
  • 1.2. Version 0.3.1
  • 1.3. Version 0.3.0
  • 1.4. Version 0.2.0
  • 1.5. Version 0.1.0
  • 1.6. Version 0.0.0
• 2. Installation
  • 2.1. User installation (without git)
  • 2.2. User installation (with git)
  • 2.3. Developer installation (with git)
  • 2.4. Documentation update (with git)
• 3. Command line interfaces
  • 3.1. Principle
  • 3.2. Command line interfaces common options
• 4. ascidian_atlas
  • 4.1. ascidian_atlas additional options
  • 4.2. Assess the quality of a set of named ascidian embryos
  • 4.3. Handling property files
    • 4.3.1. Computing cell fates
• 5. ascidian_atlas_init_naming
  • 5.1. ascidian_atlas_init_naming additional options
  • 5.2. Initial naming of an embryo
• 6. ascidian_atlas_naming
  • 6.1. ascidian_atlas_naming additional options
  • 6.2. Naming propagation for an embryo
  • 6.3. Assessing the naming procedure on an already named embryo
• 7. Image sequence properties
  • 7.1. Cell unique id
  • 7.2. Properties file format
  • 7.3. Properties
    • 7.3.1. Morphometric properties
    • 7.3.2. Ascidian dedicated properties
    • 7.3.3. Ascidian cell fates
• 8. Parameters
  • 8.1. Prefixed parameters
  • 8.2. Embryo symmetry parameters
  • 8.3. Diagnosis parameters
  • 8.4. Atlas parameters
  • 8.5. ascidian_atlas parameters
  • 8.6. Embryo registration parameters
  • 8.7. ascidian_atlas_init_naming parameters
  • 8.8. ascidian_atlas_naming parameters
• 9. Gallery
  • 9.1. Temporal alignment of cell count
  • 9.2. Temporal alignment of epidermis cell count
  • 9.3. Temporal cell composition variability
  • 9.4. Embryo volume variation
  • 9.5. Cell neighbor count
  • 9.6. Embryo symmetry axis
  • 9.7. Time interval of cell division
  • 9.8. Ordering of cell division
  • 9.9. Cell-to-cell distance along branches
  • 9.10. Cell-to-cell distances
  • 9.11. Division-to-division distances
  • 9.12. Division dendrograms
  • 9.13. Leave-one-out tests for initial naming by registration (wrt atlas count)
  • 9.14. Leave-one-out tests for initial naming by registration (wrt cell count)
  • 9.15. Division-to-division distances used to named the unnamed embryo
• 10. Reference API
  • 10.1. Algorithms
    • 10.1.1. Atlas building
    • 10.1.2. Name propagation from atlases
    • 10.1.3. Name initialization from atlases
  • 10.2. Core
    • 10.2.1. Vector distribution
• 11. Publications & bibliography