Astec package

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]. Please cite this last article if you use ASTEC.

Contents

• 1. Release notes
  • 1.1. Developer version
  • 1.2. Version 2.1.1
  • 1.3. Version 2.1.0
  • 1.4. Version 2.0.0
  • 1.5. Version 1.7.2
  • 1.6. Version 1.7.1
  • 1.7. Version 1.7.0
  • 1.8. Version 1.6.2
• 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. Data organization
• 5. astec_fusion
  • 5.1. Fusion method overview
  • 5.2. Important parameters in the parameter file
  • 5.3. Fusion / input data
    • 5.3.1. Input data directory names
    • 5.3.2. Input data image file names
    • 5.3.3. Fusion / input data / multichannel acquisition
  • 5.4. Fusion / output data
    • 5.4.1. Output data directory names
    • 5.4.2. Output data file names
    • 5.4.3. Fusion / output data / multichannel acquisition
  • 5.5. Step 3 parameters: raw data cropping
  • 5.6. Step 5 parameters: image co-registration
    • 5.6.1. Fusion direct strategy
    • 5.6.2. Fusion hierarchical strategy
    • 5.6.3. Acquisitions linear co-registration
    • 5.6.4. Stacks non-linear co-registration
  • 5.7. Step 6: linear combination of co-registered image stacks
  • 5.8. Step 7: fused data cropping
  • 5.9. Troubleshooting
  • 5.10. Advanced use
    • 5.10.1. Step 3: raw data cropping
• 6. astec_mars
  • 6.1. Mars method overview
  • 6.2. Mars / output data
  • 6.3. Steps 1 and 4: input image pre-processing
  • 6.4. Step 2: seed extraction
  • 6.5. Step 3: seed correction
  • 6.6. Step 5 : seeded watershed
  • 6.7. A note on parameters
• 7. astec_manualcorrection
  • 7.1. Manual correction overview
  • 7.2. Manual correction / output data
    • 7.2.1. Single segmentation file correction
    • 7.2.2. Time series segmentation files correction
  • 7.3. Segmentation correction parameters
• 8. astec_astec
  • 8.1. Astec method overview
  • 8.2. Astec / output data
  • 8.3. Input image pre-processing
  • 8.4. Step 1: \(\tilde{S}_{t}\)
  • 8.5. Step 2: \(\hat{S}_{t}\)
  • 8.6. Steps 3 and 4: volume checking
  • 8.7. Steps 5 and 6: morphosnake correction
• 9. astec_postcorrection
  • 9.1. Post-correction overview
  • 9.2. Post-correction / input data
  • 9.3. Post-correction / output data
  • 9.4. Step 1: lineage pruning
  • 9.5. Step 2: division postponing
• 10. astec_intraregistration
  • 10.1. Intra-registration procedure overview
  • 10.2. astec_intraregistration additional options
  • 10.3. Intra-registration / input data
    • 10.3.1. Intra-registration / multichannel acquisition
  • 10.4. Intra-registration / output data
  • 10.5. Step 1: co-registration
  • 10.6. Step 3: template building
  • 10.7. Step 4: resampling fusion/segmentation images
  • 10.8. Step 5: 2D+t movies
  • 10.9. Step 6: 3D maximum over the 3D+t sequence
  • 10.10. Intra-registration / parameter file examples
    • 10.10.1. Intra-registration of fusion images
    • 10.10.2. Intra-registration of segmentation images
    • 10.10.3. Intra-registration of post-segmentation images
• 11. astec_embryoproperties
  • 11.1. astec_embryoproperties additional options
  • 11.2. Extracting properties from a co-registered image sequence
  • 11.3. Embryo properties output data
  • 11.4. Handling property files
  • 11.5. Diagnosis on property file
    • 11.5.1. Contact surfaces
    • 11.5.2. Lineage
    • 11.5.3. Name
    • 11.5.4. Volume
• 12. Image sequence properties
  • 12.1. Cell unique id
  • 12.2. Properties file format
  • 12.3. Properties
    • 12.3.1. Properties computed by astec_astec
    • 12.3.2. Properties computed by astec_embryoproperties
• 13. Image preprocessing
  • 13.1. Histogram based image value transformation
  • 13.2. Membrane dedicated enhancement
  • 13.3. Outer contour
  • 13.4. Some examples
    • 13.4.1. intensity_transformation = ‘identity’ and intensity_enhancement = None
    • 13.4.2. intensity_transformation = ‘normalization_to_u8’ and intensity_enhancement = None
    • 13.4.3. intensity_transformation = ‘identity’ and intensity_enhancement = ‘gace’
    • 13.4.4. intensity_transformation = ‘normalization_to_u8’ and intensity_enhancement = ‘gace’
    • 13.4.5. intensity_transformation = None and intensity_enhancement = ‘gace’
• 14. Parameters
  • 14.1. Prefixed parameters
  • 14.2. Common parameters
  • 14.3. Data organisation parameters
  • 14.4. Ace parameters
  • 14.5. Morphosnake parameters
  • 14.6. Preprocessing parameters
  • 14.7. Registration parameters
  • 14.8. Seed edition parameters
  • 14.9. Watershed parameters
  • 14.10. Diagnosis parameters
  • 14.11. astec_fusion parameters
  • 14.12. astec_intraregistration parameters
  • 14.13. astec_mars parameters
  • 14.14. astec_manualcorrection parameters
  • 14.15. astec_astec parameters
  • 14.16. astec_postcorrection parameters
• 15. Some notations
• 16. Reference API
  • 16.1. Fusion
  • 16.2. Mars
  • 16.3. Manual correction
  • 16.4. Astec
  • 16.5. Post correction
  • 16.6. Motion compensation aka intra-registration
• 17. Publications & bibliography