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.
astec_fusion
- 5.1. Fusion method overview
- 5.2. Multiview lightsheet microscope acquisition
- 5.3. Important parameters in the parameter file
- 5.4. Fusion / input data
- 5.5. Fusion / output data
- 5.6. Step 3 parameters: raw data cropping
- 5.7. Step 5 parameters: image co-registration
- 5.8. Step 6: linear combination of co-registered image stacks
- 5.9. Step 7: fused data cropping
- 5.10. Fusion troubleshooting
- 5.11. Advanced use
- 6.
astec_drift
- 7.
astec_mars
- 8.
astec_manualcorrection
- 9.
astec_astec
- 10.
astec_postcorrection
- 11.
astec_intraregistration
- 11.1. Intra-registration procedure overview
- 11.2.
astec_intraregistration
additional options - 11.3. Intra-registration / input data
- 11.4. Intra-registration / output data
- 11.5. Step 1: co-registration
- 11.6. Step 3: template building
- 11.7. Step 4: resampling fusion/segmentation images
- 11.8. Step 5: 2D+t movies
- 11.9. Step 6: 3D maximum over the 3D+t sequence
- 11.10. Intra-registration / parameter file examples
- 12.
astec_embryoproperties
- 13. Image sequence properties
- 14. Image preprocessing
- 14.1. Histogram based image value transformation
- 14.2. Membrane dedicated enhancement
- 14.3. Outer contour
- 14.4. Some examples
- 14.4.1.
intensity_transformation
= ‘identity’ andintensity_enhancement
= None - 14.4.2.
intensity_transformation
= ‘normalization_to_u8’ andintensity_enhancement
= None - 14.4.3.
intensity_transformation
= ‘identity’ andintensity_enhancement
= ‘gace’ - 14.4.4.
intensity_transformation
= ‘normalization_to_u8’ andintensity_enhancement
= ‘gace’ - 14.4.5.
intensity_transformation
= None andintensity_enhancement
= ‘gace’
- 14.4.1.
- 15. Image registration
- 16. Parameters
- 16.1. Prefixed parameters
- 16.2. Experiment parameters
- 16.2.1. Common parameters
- 16.2.2. Raw data directory parameters
- 16.2.3. Fusion directory parameters
- 16.2.4. Drift directory parameters
- 16.2.5. Contour directory parameters
- 16.2.6. Membrane reconstruction directory parameters
- 16.2.7. Seed reconstruction directory parameters
- 16.2.8. Morphosnake reconstruction directory parameters
- 16.2.9. Mars directory parameters
- 16.2.10. Astec directory parameters
- 16.2.11. Post-processing directory parameters
- 16.2.12. Intra-registration directory parameters
- 16.3. Ace parameters
- 16.4. Morphosnake parameters
- 16.5. Preprocessing parameters
- 16.6. Registration parameters
- 16.7. Seed edition parameters
- 16.8. Watershed parameters
- 16.9. Diagnosis parameters
- 16.10.
astec_fusion
parameters - 16.11.
astec_drift
parameters - 16.12.
astec_intraregistration
parameters - 16.13.
astec_mars
parameters - 16.14.
astec_manualcorrection
parameters - 16.15.
astec_astec
parameters - 16.16.
astec_postcorrection
parameters
- 17. Some notations
- 18. Reference API
- 19. Release notes
- 19.1. Developer version
- 19.2. Version 2.2.11
- 19.3. Version 2.2.10
- 19.4. Version 2.2.9
- 19.5. Version 2.2.8
- 19.6. Version 2.2.7
- 19.7. Version 2.2.6
- 19.8. Version 2.2.5
- 19.9. Version 2.2.4
- 19.10. Version 2.2.3
- 19.11. Version 2.2.2
- 19.12. Version 2.2.1
- 19.13. Version 2.2.0
- 19.14. Version 2.1.11
- 19.15. Version 2.1.10
- 19.16. Version 2.1.9
- 19.17. Version 2.1.8
- 19.18. Version 2.1.7
- 19.19. Version 2.1.6
- 19.20. Version 2.1.5
- 19.21. Version 2.1.4
- 19.22. Version 2.1.3
- 19.23. Version 2.1.2
- 19.24. Version 2.1.1
- 19.25. Version 2.1.0
- 19.26. Version 2.0.0
- 19.27. Version 1.7.2
- 19.28. Version 1.7.1
- 19.29. Version 1.7.0
- 19.30. Version 1.6.2
- 20. Publications & bibliography