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.

Related publications can be found in Publications & bibliography.

Contents

• 1. Overview
• 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. Tutorial
  • 5.1. Fusion parameter settings
    • 5.1.1. Setting acquisition_mirrors
    • 5.1.2. Setting acquisition_leftcamera_z_stacking
    • 5.1.3. Setting acquisition_orientation
  • 5.2. Fusion (example)
  • 5.3. Drift compensated fusion
    • 5.3.1. Stack #0 fusion (parameters)
    • 5.3.2. Stack #1 fusion (parameters)
    • 5.3.3. Drift estimation of stack #0 (parameters)
    • 5.3.4. Drift estimation of stack #1 (parameters)
    • 5.3.5. Drift estimation between stacks (parameters)
    • 5.3.6. Drift compensated fusion (parameters)
• 6. Tutorial (advanced)
  • 6.1. Fusion with missing slices (without drift)
  • 6.2. Drift compensated fusion with missing slices (DCFMS)
    • 6.2.1. Stacks fusion (DCFMS)
    • 6.2.2. Drift estimation within stacks (DCFMS)
    • 6.2.3. Drift estimation between stacks (DCFMS)
    • 6.2.4. Drift compensated fusion (DCFMS)
• 7. astec_fusion
  • 7.1. Fusion method overview
  • 7.2. Multiview lightsheet microscope acquisition
  • 7.3. Important parameters in the parameter file
  • 7.4. Fusion / input data
    • 7.4.1. Input data directory names
    • 7.4.2. Input data image file names
    • 7.4.3. Input data organization examples
    • 7.4.4. Fusion / input data / multichannel acquisition
  • 7.5. Fusion / output data
    • 7.5.1. Output data directory names
    • 7.5.2. Output data file names
    • 7.5.3. Fusion / output data / multichannel acquisition
  • 7.6. Step 3 parameters: raw data cropping
  • 7.7. Step 5 parameters: image co-registration
    • 7.7.1. Fusion direct strategy
    • 7.7.2. Fusion hierarchical strategy
    • 7.7.3. Acquisitions linear co-registration
    • 7.7.4. Stacks non-linear co-registration
  • 7.8. Step 6: linear combination of co-registered image stacks
  • 7.9. Step 7: fused data cropping
  • 7.10. Fusion troubleshooting
    • 7.10.1. Fusion strategy / transformation tuning
  • 7.11. Advanced use
    • 7.11.1. Step 3: raw data cropping
• 8. astec_drift
  • 8.1. Registration score
  • 8.2. Drift prerequisite
  • 8.3. Drift / output data
  • 8.4. Drift / principle
  • 8.5. Drift / selection of corrections
  • 8.6. Drift / computation of corrections
  • 8.7. Drift / inter-stack registration
  • 8.8. Drift / disk cleaning
• 9. astec_mars
  • 9.1. Mars method overview
  • 9.2. Mars / output data
  • 9.3. Steps 1 and 4: input image pre-processing
  • 9.4. Step 2: seed extraction
  • 9.5. Step 3: seed correction
  • 9.6. Step 5 : seeded watershed
  • 9.7. A note on parameters
  • 9.8. Mars: parameter file example
• 10. astec_manualcorrection
  • 10.1. Manual correction overview
  • 10.2. Manual correction / output data
    • 10.2.1. Single segmentation file correction
    • 10.2.2. Time series segmentation files correction
  • 10.3. Segmentation correction parameters
• 11. astec_astec
  • 11.1. Astec method overview
  • 11.2. Astec / output data
  • 11.3. Input image pre-processing
  • 11.4. Step 1: \(\tilde{S}_{t}\)
  • 11.5. Step 2: \(\hat{S}_{t}\)
  • 11.6. Steps 3 and 4: volume checking
  • 11.7. Steps 5 and 6: morphosnake correction
  • 11.8. Astec troubleshooting
    • 11.8.1. Tuning parameters to avoid over-segmentations
  • 11.9. Astec parameter file examples
    • 11.9.1. Segmentation backward propagation
• 12. astec_postcorrection
  • 12.1. Post-correction overview
  • 12.2. Post-correction / input data
  • 12.3. Post-correction / output data
  • 12.4. Step 1: lineage pruning
  • 12.5. Step 2: division postponing
• 13. astec_intraregistration
  • 13.1. Intra-registration procedure overview
  • 13.2. astec_intraregistration additional options
  • 13.3. Intra-registration / input data
    • 13.3.1. Intra-registration / multichannel acquisition
  • 13.4. Intra-registration / output data
  • 13.5. Step 1: co-registration
  • 13.6. Step 3: template building
  • 13.7. Step 4: resampling fusion/segmentation images
  • 13.8. Step 5: 2D+t movies
  • 13.9. Step 6: 3D maximum over the 3D+t sequence
  • 13.10. Intra-registration / parameter file examples
    • 13.10.1. Intra-registration of fusion images
    • 13.10.2. Intra-registration of segmentation images
    • 13.10.3. Intra-registration of post-segmentation images
  • 13.11. Intra-registration troubleshooting
• 14. astec_embryoproperties
  • 14.1. astec_embryoproperties additional options
  • 14.2. Extracting properties from a co-registered image sequence
  • 14.3. Embryo properties output data
  • 14.4. Handling property files
  • 14.5. Diagnosis on property file
    • 14.5.1. Contact surfaces
    • 14.5.2. Lineage
    • 14.5.3. Name
    • 14.5.4. Volume
• 15. Image sequence properties
  • 15.1. Cell unique id
  • 15.2. Properties file format
  • 15.3. Properties
    • 15.3.1. Properties computed by astec_astec and astec_postprocessing
    • 15.3.2. Properties computed by astec_embryoproperties
• 16. Image preprocessing
  • 16.1. Histogram based image value transformation
  • 16.2. Intensity image smoothing
  • 16.3. Membrane dedicated enhancement
  • 16.4. Outer contour
  • 16.5. Some examples
    • 16.5.1. intensity_transformation = ‘identity’ and intensity_enhancement = None
    • 16.5.2. intensity_transformation = ‘normalization_to_u8’ and intensity_enhancement = None
    • 16.5.3. intensity_transformation = ‘identity’ and intensity_enhancement = ‘gace’
    • 16.5.4. intensity_transformation = ‘normalization_to_u8’ and intensity_enhancement = ‘gace’
    • 16.5.5. intensity_transformation = None and intensity_enhancement = ‘gace’
• 17. Image registration
  • 17.1. Image-to-image registration
  • 17.2. Stack-to-stack registration
• 18. Parameters
  • 18.1. Prefixed parameters
  • 18.2. Experiment parameters
    • 18.2.1. Common parameters
    • 18.2.2. Raw data directory parameters
    • 18.2.3. Fusion directory parameters
    • 18.2.4. Drift directory parameters
    • 18.2.5. Contour directory parameters
    • 18.2.6. Membrane reconstruction directory parameters
    • 18.2.7. Seed reconstruction directory parameters
    • 18.2.8. Morphosnake reconstruction directory parameters
    • 18.2.9. Mars directory parameters
    • 18.2.10. Astec directory parameters
    • 18.2.11. Post-processing directory parameters
    • 18.2.12. Intra-registration directory parameters
  • 18.3. Ace parameters
  • 18.4. Morphosnake parameters
  • 18.5. Preprocessing parameters
  • 18.6. Registration parameters
  • 18.7. Seed edition parameters
  • 18.8. Watershed parameters
  • 18.9. Diagnosis parameters
  • 18.10. astec_fusion parameters
  • 18.11. astec_drift parameters
  • 18.12. astec_mars parameters
  • 18.13. astec_manualcorrection parameters
  • 18.14. astec_astec parameters
  • 18.15. astec_postcorrection parameters
  • 18.16. astec_intraregistration parameters
  • 18.17. astec_embryoproperties parameters
• 19. Some notations
• 20. Reference API
  • 20.1. Fusion
  • 20.2. Mars
  • 20.3. Manual correction
  • 20.4. Astec
  • 20.5. Post correction
  • 20.6. Motion compensation aka intra-registration
• 21. Release notes
  • 21.1. Developer version
  • 21.2. Version 2.3.10
  • 21.3. Version 2.3.9
  • 21.4. Version 2.3.8
  • 21.5. Version 2.3.7
  • 21.6. Version 2.3.6
  • 21.7. Version 2.3.5
  • 21.8. Version 2.3.4
  • 21.9. Version 2.3.3
  • 21.10. Version 2.3.2
  • 21.11. Version 2.3.1
  • 21.12. Version 2.3.0
  • 21.13. Version 2.2.13
  • 21.14. Version 2.2.12
  • 21.15. Version 2.2.11
  • 21.16. Version 2.2.10
  • 21.17. Version 2.2.9
  • 21.18. Version 2.2.8
  • 21.19. Version 2.2.7
  • 21.20. Version 2.2.6
  • 21.21. Version 2.2.5
  • 21.22. Version 2.2.4
  • 21.23. Version 2.2.3
  • 21.24. Version 2.2.2
  • 21.25. Version 2.2.1
  • 21.26. Version 2.2.0
  • 21.27. Version 2.1.11
  • 21.28. Version 2.1.10
  • 21.29. Version 2.1.9
  • 21.30. Version 2.1.8
  • 21.31. Version 2.1.7
  • 21.32. Version 2.1.6
  • 21.33. Version 2.1.5
  • 21.34. Version 2.1.4
  • 21.35. Version 2.1.3
  • 21.36. Version 2.1.2
  • 21.37. Version 2.1.1
  • 21.38. Version 2.1.0
  • 21.39. Version 2.0.0
  • 21.40. Version 1.7.2
  • 21.41. Version 1.7.1
  • 21.42. Version 1.7.0
  • 21.43. Version 1.6.2
• 22. Publications & bibliography