Welcome to astec’s documentation!

ASTEC, for Adaptive Segmentation and Tracking of Embryonic Cells, was first developed during L. Guignard PhD thesis [Gui15].

Its development has been pursued, and it was used to process 3D+t movies acquired by the MuViSPIM light-sheet microscope [GFL+20].

Contents

• 1. Installation
  • 1.1. User installation (without git)
  • 1.2. User installation (with git)
  • 1.3. Developer installation (with git)
• 2. Command line interfaces
  • 2.1. Data organization
  • 2.2. Principle
  • 2.3. Command line interfaces common options
• 3. astec_fusion
  • 3.1. Fusion method overview
  • 3.2. Important parameters in the parameter file
  • 3.3. Fusion / input data
    • 3.3.1. Input data directory names
    • 3.3.2. Input data image file names
    • 3.3.3. Fusion / input data / multichannel acquisition
  • 3.4. Fusion / output data
    • 3.4.1. Output data directory names
    • 3.4.2. Output data file names
    • 3.4.3. Fusion / output data / multichannel acquisition
  • 3.5. Step 3 parameters: raw data cropping
  • 3.6. Step 5 parameters: image co-registration
    • 3.6.1. Fusion direct strategy
    • 3.6.2. Fusion hierarchical strategy
    • 3.6.3. Acquisitions linear co-registration
    • 3.6.4. Stacks non-linear co-registration
  • 3.7. Step 6: linear combination of co-registered image stacks
  • 3.8. Step 7: fused data cropping
  • 3.9. Troubleshooting
  • 3.10. Advanced use
    • 3.10.1. Step 3: raw data cropping
• 4. astec_mars
  • 4.1. Mars method overview
  • 4.2. Mars / output data
  • 4.3. Steps 1 and 4: input image pre-processing
  • 4.4. Step 2: seed extraction
  • 4.5. Step 3: seed correction
  • 4.6. Step 5 : seeded watershed
• 5. astec_manualcorrection
  • 5.1. Manual correction overview
  • 5.2. Manual correction / output data
    • 5.2.1. Single segmentation file correction
    • 5.2.2. Time series segmentation files correction
  • 5.3. Segmentation correction parameters
• 6. astec_astec
  • 6.1. Astec method overview
  • 6.2. Astec / output data
  • 6.3. Input image pre-processing
  • 6.4. Step 1: \(\tilde{S}_{t}\)
  • 6.5. Step 2: \(\hat{S}_{t}\)
  • 6.6. Steps 3 and 4: volume checking
  • 6.7. Steps 5 and 6: morphosnake correction
• 7. astec_postcorrection
  • 7.1. Post-correction overview
  • 7.2. Post-correction / input data
  • 7.3. Post-correction / output data
  • 7.4. Step 1: lineage pruning
  • 7.5. Step 2: division postponing
• 8. astec_intraregistration
  • 8.1. Intra-registration procedure overview
  • 8.2. astec_intraregistration additional options
  • 8.3. Intra-registration / input data
    • 8.3.1. Intra-registration / multichannel acquisition
  • 8.4. Intra-registration / output data
  • 8.5. Step 1: co-registration
  • 8.6. Step 3: template building
  • 8.7. Step 4: resampling fusion/segmentation images
  • 8.8. Step 5: 2D+t movies
  • 8.9. Step 6: 3D maximum over the 3D+t sequence
• 9. astec_embryoproperties
  • 9.1. astec_embryoproperties additional options
  • 9.2. Extracting properties from a co-registered image sequence
  • 9.3. Embryo properties output data
  • 9.4. Handling property files
  • 9.5. Diagnosis on property file
    • 9.5.1. Contact surfaces
    • 9.5.2. Lineage
    • 9.5.3. Name
    • 9.5.4. Volume
• 10. astec_atlas
  • 10.1. astec_atlas additional options
  • 10.2. astec_atlas principle
• 11. astec_atlas_naming
  • 11.1. astec_atlas_naming additional options
  • 11.2. Naming propagation for an embryo
  • 11.3. Assessing the naming procedure on an already named embryo
• 12. Image preprocessing
  • 12.1. Histogram based image value transformation
  • 12.2. Membrane dedicated enhancement
  • 12.3. Parameter list
• 13. Parameters
  • 13.1. Prefixed parameters
  • 13.2. Common parameters
  • 13.3. Data organisation parameters
  • 13.4. Ace parameters
  • 13.5. Morphosnake parameters
  • 13.6. Preprocessing parameters
  • 13.7. Registration parameters
  • 13.8. Seed edition parameters
  • 13.9. Watershed parameters
  • 13.10. astec_fuse parameters
  • 13.11. astec_intraregistration parameters
  • 13.12. astec_mars parameters
  • 13.13. astec_manualcorrection parameters
  • 13.14. astec_astec parameters
  • 13.15. astec_postcorrection parameters
  • 13.16. Diagnosis parameters
  • 13.17. Embryo symmetry parameters
  • 13.18. Atlas parameters
  • 13.19. astec_atlas parameters
  • 13.20. astec_atlas_naming parameters
  • 13.21. Embryo registration parameters
  • 13.22. astec_atlas_init_naming parameters
• 14. Overview
  • 14.1. Notations
• 15. Reference API
  • 15.1. Fusion
  • 15.2. Mars
  • 15.3. Manual correction
  • 15.4. Astec
  • 15.5. Post correction
  • 15.6. Motion compensation aka intra-registration
  • 15.7. Atlas building
  • 15.8. Name propagation from atlases
  • 15.9. Name initialization from atlases
• 16. Publications & bibliography