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
- 2. Command line interfaces
- 3.
astec_fusion
- 3.1. Fusion method overview
- 3.2. Important parameters in the parameter file
- 3.3. Fusion / input data
- 3.4. Fusion / output data
- 3.5. Step 3 parameters: raw data cropping
- 3.6. Step 5 parameters: image 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
- 4.
astec_mars
- 5.
astec_manualcorrection
- 6.
astec_astec
- 7.
astec_postcorrection
- 8.
astec_intraregistration
- 8.1. Intra-registration procedure overview
- 8.2.
astec_intraregistration
additional options - 8.3. Intra-registration / input data
- 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
- 10.
astec_atlas
- 11.
astec_atlas_naming
- 12.
astec_atlas_init_naming
- 13. Image preprocessing
- 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.
astec_fuse
parameters - 14.11.
astec_intraregistration
parameters - 14.12.
astec_mars
parameters - 14.13.
astec_manualcorrection
parameters - 14.14.
astec_astec
parameters - 14.15.
astec_postcorrection
parameters - 14.16. Diagnosis parameters
- 14.17. Embryo symmetry parameters
- 14.18. Atlas parameters
- 14.19.
astec_atlas
parameters - 14.20.
astec_atlas_naming
parameters - 14.21. Embryo registration parameters
- 14.22.
astec_atlas_init_naming
parameters
- 15. Overview
- 16. Reference API
- 17. Publications & bibliography