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. Installation
- 2. Command line interfaces
- 3. Data organization
- 4. Tutorial
- 5. Tutorial (advanced)
- 6.
astec_fusion
- 6.1. Fusion method overview
- 6.2. Multiview lightsheet microscope acquisition
- 6.3. Important parameters in the parameter file
- 6.4. Fusion / input data
- 6.5. Fusion / output data
- 6.6. Step 3 parameters: raw data cropping
- 6.7. Step 5 parameters: image co-registration
- 6.8. Step 6: linear combination of co-registered image stacks
- 6.9. Step 7: fused data cropping
- 6.10. Fusion troubleshooting
- 6.11. Advanced use
- 7.
astec_drift
- 8.
astec_mars
- 9.
astec_manualcorrection
- 10.
astec_astec
- 11.
astec_postcorrection
- 12.
astec_intraregistration
- 12.1. Intra-registration procedure overview
- 12.2.
astec_intraregistration
additional options - 12.3. Intra-registration / input data
- 12.4. Intra-registration / output data
- 12.5. Step 1: co-registration
- 12.6. Step 3: template building
- 12.7. Step 4: resampling fusion/segmentation images
- 12.8. Step 5: 2D+t movies
- 12.9. Step 6: 3D maximum over the 3D+t sequence
- 12.10. Intra-registration / parameter file examples
- 13.
astec_embryoproperties
- 14. Image sequence properties
- 15. Image preprocessing
- 15.1. Histogram based image value transformation
- 15.2. Membrane dedicated enhancement
- 15.3. Outer contour
- 15.4. Some examples
- 15.4.1.
intensity_transformation
= ‘identity’ andintensity_enhancement
= None - 15.4.2.
intensity_transformation
= ‘normalization_to_u8’ andintensity_enhancement
= None - 15.4.3.
intensity_transformation
= ‘identity’ andintensity_enhancement
= ‘gace’ - 15.4.4.
intensity_transformation
= ‘normalization_to_u8’ andintensity_enhancement
= ‘gace’ - 15.4.5.
intensity_transformation
= None andintensity_enhancement
= ‘gace’
- 15.4.1.
- 16. Image registration
- 17. Parameters
- 17.1. Prefixed parameters
- 17.2. Experiment parameters
- 17.2.1. Common parameters
- 17.2.2. Raw data directory parameters
- 17.2.3. Fusion directory parameters
- 17.2.4. Drift directory parameters
- 17.2.5. Contour directory parameters
- 17.2.6. Membrane reconstruction directory parameters
- 17.2.7. Seed reconstruction directory parameters
- 17.2.8. Morphosnake reconstruction directory parameters
- 17.2.9. Mars directory parameters
- 17.2.10. Astec directory parameters
- 17.2.11. Post-processing directory parameters
- 17.2.12. Intra-registration directory parameters
- 17.3. Ace parameters
- 17.4. Morphosnake parameters
- 17.5. Preprocessing parameters
- 17.6. Registration parameters
- 17.7. Seed edition parameters
- 17.8. Watershed parameters
- 17.9. Diagnosis parameters
- 17.10.
astec_fusion
parameters - 17.11.
astec_drift
parameters - 17.12.
astec_intraregistration
parameters - 17.13.
astec_mars
parameters - 17.14.
astec_manualcorrection
parameters - 17.15.
astec_astec
parameters - 17.16.
astec_postcorrection
parameters
- 18. Some notations
- 19. Reference API
- 20. Release notes
- 20.1. Developer version
- 20.2. Version 2.2.13
- 20.3. Version 2.2.12
- 20.4. Version 2.2.11
- 20.5. Version 2.2.10
- 20.6. Version 2.2.9
- 20.7. Version 2.2.8
- 20.8. Version 2.2.7
- 20.9. Version 2.2.6
- 20.10. Version 2.2.5
- 20.11. Version 2.2.4
- 20.12. Version 2.2.3
- 20.13. Version 2.2.2
- 20.14. Version 2.2.1
- 20.15. Version 2.2.0
- 20.16. Version 2.1.11
- 20.17. Version 2.1.10
- 20.18. Version 2.1.9
- 20.19. Version 2.1.8
- 20.20. Version 2.1.7
- 20.21. Version 2.1.6
- 20.22. Version 2.1.5
- 20.23. Version 2.1.4
- 20.24. Version 2.1.3
- 20.25. Version 2.1.2
- 20.26. Version 2.1.1
- 20.27. Version 2.1.0
- 20.28. Version 2.0.0
- 20.29. Version 1.7.2
- 20.30. Version 1.7.1
- 20.31. Version 1.7.0
- 20.32. Version 1.6.2
- 21. Publications & bibliography