Ascidian package

The ASCIDIAN package aims at exploiting results issued from the processing of 3D+t sequences of developing embryos imaged by a light-sheet microscope. The processing, done by the ASTEC suite, results in a so-called property file.

Assuming the imaged embryos are ascidians, this suite provides tools to name (after Conklin) one particular time point (see ascidian_naming_timepoint), to propagate the naming to other time points (see ascidian_naming_propagation), or to study a population of embryos (see ascidian_embryo and Gallery).

Contents

• 1. Installation
  • 1.1. User installation (without git)
  • 1.2. User installation (with git)
  • 1.3. Developer installation (with git)
  • 1.4. Documentation update (with git)
• 2. Command line interfaces
  • 2.1. Principle
  • 2.2. Command line interfaces common options
• 3. ascidian_embryo
  • 3.1. ascidian_embryo additional options
  • 3.2. Assess the quality of a set of named ascidian embryos
  • 3.3. Examples of use
    • 3.3.1. Computing cell fates
    • 3.3.2. Computing color map from cell names
    • 3.3.3. Calibration of the time post fertilization (tpf) and time interval
    • 3.3.4. Writing morphonet files
• 4. ascidian_naming_timepoint
  • 4.1. ascidian_naming_timepoint additional options
  • 4.2. Initial naming of an embryo
  • 4.3. Initial naming: parameter file examples
    • 4.3.1. Use of transformation_filename
  • 4.4. Initial naming: Morphonet dedicated generated field
• 5. ascidian_naming_propagation
  • 5.1. ascidian_naming_propagation additional options
  • 5.2. Naming propagation for an embryo
  • 5.3. Naming propagation: Morphonet dedicated generated field
  • 5.4. Assessing the naming procedure on an already named embryo
• 6. Image sequence properties
  • 6.1. Cell unique id
  • 6.2. Properties file format
  • 6.3. Properties
    • 6.3.1. Morphometric properties
    • 6.3.2. Ascidian dedicated properties
    • 6.3.3. Ascidian cell fates
• 7. Parameters
  • 7.1. Prefixed parameters
  • 7.2. Diagnosis parameters
  • 7.3. Embryo symmetry parameters
  • 7.4. Figure parameters
  • 7.5. Base parameters
  • 7.6. Naming propagation parameters
  • 7.7. Embryo registration parameters
  • 7.8. Naming assignment parameters
  • 7.9. Naming timepoint parameters
• 8. Gallery
  • 8.1. Embryo set assessment
    • 8.1.1. Temporal alignment of embryo development
    • 8.1.2. Volume normalization of embryos
    • 8.1.3. Cell composition
    • 8.1.4. Cell neighbor count
    • 8.1.5. Division time differences
    • 8.1.6. Division time mis-ordering: couple of division view
    • 8.1.7. Division time mis-ordering: global view
  • 8.2. Embryo symmetry assessment
    • 8.2.1. Detection of the symmetry axis
    • 8.2.2. Detection of symmetrical cells
  • 8.3. Naming one time point
    • 8.3.1. Naming one time point by embryo co-registration
    • 8.3.2. Naming one time point by cell signature
  • 8.4. Contact surface based cell-to-cell distance
    • 8.4.1. Cell-to-cell distance along branches
    • 8.4.2. Cell-to-cell distance for same, sister or other cells
  • 8.5. Contact surface based division-to-division distance
    • 8.5.1. Division-to-division distance for right/wrong cell pairings
    • 8.5.2. Dendrograms from division-to-division distances
• 9. Reference API
• 10. Release notes
  • 10.1. Developer version
  • 10.2. Version 1.1.12
  • 10.3. Version 1.1.11
  • 10.4. Version 1.1.10
  • 10.5. Version 1.1.9
  • 10.6. Version 1.1.8
  • 10.7. Version 1.1.7
  • 10.8. Version 1.1.6
  • 10.9. Version 1.1.5
  • 10.10. Version 1.1.4
  • 10.11. Version 1.1.3
  • 10.12. Version 1.1.2
  • 10.13. Version 1.1.1
  • 10.14. Version 1.1.0
  • 10.15. Version 1.0.0
  • 10.16. Version 0.3.1
  • 10.17. Version 0.3.0
  • 10.18. Version 0.2.0
  • 10.19. Version 0.1.0
  • 10.20. Version 0.0.0
• 11. Publications & bibliography