4. Data organization

It is assumed that there will be one directory per experiment (ie per embryo). This directory contains the acquired data, but will also contain the result data as depicted below.

$ /path/to/experiment/
├── RAWDATA/
│  └── ...
├── FUSE/
│  └── FUSE_<EXP_FUSE>/
│      ├── ...
│      └── LOGS/
├── CONTOUR/
│   └── ...
├── SEG/
│  └── SEG_<EXP_SEG>/
│      ├── ...
│      └── LOGS/
├── POST/
│  └── POST_<EXP_POST>/
│      ├── ...
│      └── LOGS/
├── REC-MEMBRANE/
│   └── REC_<EXP_RECONSTRUCTION>/
├── REC-SEED/
│   └── REC_<EXP_RECONSTRUCTION>/
├── REC-MORPHOSNAKE/
│   └── REC_<EXP_RECONSTRUCTION>/
└── INTRAREG/
   └── INTRAREG_<EXP_INTRAREG>/
       ├── ...
       └── LOGS/

  • RAWDATA/ contains the raw acquisitions issued from the microscope. See section Fusion / input data for their organization.

  • FUSE/ will contain the images after fusion of the raw data. See section astec_fusion for details.

  • CONTOUR/ may contain outer contour images (to alleviate their poor contrast). See section Outer contour for details.

  • SEG/ will contain the images after segmentation. For the segmentation of one time point (independently from the others, typically the first time point), see section astec_mars. For the segmentation by propagation (from an already segmented time point), see section astec_astec.

  • POST/ will contain the images after post-segmentation. See section astec_postcorrection for details.

  • REC-MEMBRANE/, REC-SEED/, and REC-MORPHOSNAKE/ will contains the fusion image after pre-processing (may include intensity rescaling, membrane enhancement, fusion of outer contour, etc). These pre-processed images are generated at the same time than the segmentation images. See section Image preprocessing for details.

  • INTRAREG/ will contain the images after drift compensation. See section astec_intraregistration for details.

  • ..._<EXP_XXX>/ To compared different experiments (different settings), results are stored into subdirectories whose suffix can be set by the user.

  • .../LOGS/ This subdirectory contains an history of the commands launched to generate the results, as well as a copy of the parameter file (suffixed by date and time) and the log of the execution (suffixed by the same date and time).