5. astec_manualcorrection

5.1. Manual correction overview

astec_manualcorrection aims at correcting segmentation errors, either for a single image, as the one produced by astec_mars (see astec_mars), or a series of images, as the ones produced by astec_astec (see astec_astec).

The seeded watershed is likely to produce segmentation errors, even with a careful choice of parameters. It is advised to set the parameters to favour over-segmentations insted of under-segmentations since the former are much more easier to correct, which is the purpose of astec_manualcorrection.

When dealing with a single image produced by astec_mars, the segmentation error correction could also be done at the seed correction step (see Step 3: seed correction) where seeds can be fused, or new seeds can be added (by specifying point coordinate): see the seed_edition_file variable for details in section Seed edition parameters.

Here, a under-segmented cell can be splitted by changing the parameters controling the search for seeds by \(h\)-minima computation for the indicated cells, ie watershed_seed_hmin_min_value, watershed_seed_hmin_max_value, and watershed_seed_hmin_delta_value. The \(h\)-minima computation start with a \(h\) of watershed_seed_hmin_max_value until two seeds are found inside the cell of interest. Then, a watershed is performed to get the final splitting of the cell.

Note

It is then mandatory to have the fusion image at hand. Seeds are computed from the dedicated pre-processed image (preprocessing parameters, see section Preprocessing parameters, eventually prefixed by seed_, see section astec_astec parameters), and the watershed will be computed onto the dedicated pre-processed image (preprocessing parameters, see section Preprocessing parameters, eventually prefixed by membrane_). Thus, it is adviced to keep these pre-processed images with keep_reconstruction = True in the parameter file when running astec_astec. Both pre-processed images being named after the fusion image, they can not be retrieved if the fusion image is not available. If not available, the pre-processed image(s) will be recomputed from the fusion images.

See section astec_manualcorrection parameters for a detailed presentation of the mapping file, to specify cells to be fused or cells to be splitted.

For time series, newly formed divisions are propagated along the time series and embryo properties are updated (only cell lineage and cell volume are updated, other properties, that may become wrong, are deleted). The division propagation is done as in step 1 of astec_astec (see Step 1: \tilde{S}_{t})

  1. Segmentation of previous time point is deformed onto the current time point.

  2. Cells are eroded to get two seeds inside the cell to be divided.

  3. Segmentation (watershed-based) from the deformed seeds.

This propagation only changes the progeny of the cell(s) to be splitted. Other cells remain unchanged.

Since pre-processed images (see Input image pre-processing) are used either for seed computation (as in Step 2: \hat{S}_{t}) or for watershed segmentation, it is adviced to keep the pro-processed images by setting keep_reconstruction to True.

5.2. Manual correction / output data

5.2.1. Single segmentation file correction

The historical used of astec_manualcorrection was to correct the segmentation image issued from astec_mars to provide a good initialization (a good first segmentation image) to astec_astec. Hence, the file issued from astec_mars, namely <EN>_mars_t<begin>.inr, was transformed into a file with a different name, namely``<EN>_seg_t<begin>.inr``.

The result can then be stored in the same sub-directory SEG/SEG_<EXP_SEG> under the /path/to/experiment/ directory where <EXP_SEG> is the value of the variable EXP_SEG (its default value is ‘RELEASE’).

/path/to/experiment/
├── ...
├── SEG/
│  └── SEG_<EXP_SEG>/
│     ├── <EN>_mars_t<begin>.inr
│     ├── <EN>_seg_t<begin>.inr
│     ├── LOGS/
│     └── RECONSTRUCTION/
...

However, it is also possible to change the name of the result directory, as detailed below.

5.2.2. Time series segmentation files correction

A time series of segmentation images can also be corrected. Here the segmentation files from the sub-directory SEG/SEG_<EXP_SEG_FROM> are corrected into the SEG/SEG_<EXP_SEG_TO>. The property file is updated. Only the cell lineage and volumes are updated, other properties are deleted and should be recomputed with astec_embryoproperties once the corrections are done.

/path/to/experiment/
├── ...
├── SEG/
│  ├── SEG_<EXP_SEG_FROM>/
│  │  ├── <EN>_seg_lineage.xml
│  │  ├── <EN>_seg_t<begin>.inr
│  │  ├── ...
│  │  ├── <EN>_seg_t<end>.inr
│  │  ├── LOGS/
│  │  └── RECONSTRUCTION/
│  └─ SEG_<EXP_SEG_TO>/
│     ├── <EN>_seg_lineage.xml
│     ├── <EN>_seg_t<begin>.inr
│     ├── ...
│     ├── <EN>_seg_t<end>.inr
│     ├── LOGS/
│     └── RECONSTRUCTION/
...

5.3. Segmentation correction parameters

astec_manualcorrection parses a correction file whose name is given by the variable manualcorrection_file. The syntax of this file is described in section astec_manualcorrection parameters. See also the tutorial section for an other example.