13. astec_atlas_naming

astec_atlas_naming can be used either to name an ascidian embryo (for which the lineage and the contact surfaces are known, and one time point is already named), or to evaluate the naming on an already named embryo.

Section astec_atlas_naming parameters provides a view on all the parameters.

13.1. astec_atlas_naming additional options

The following options are available:

-write-selection, --write-selection

write out morphonet selection files

13.2. Naming propagation for an embryo

To name an embryo, the minimal parameter file has to contain:

  • the input property file, containing the lineage, the contact surfaces, and some names (typically a 64-cells time point has to be named),

  • the output property file,

  • the list of atlases (already named embryos).

inputFile = 'property_file_partially_named.xml'
outputFile = 'property_file_named_after_the_atlases.xml'

atlasFiles = []
atlasFiles += ['/path_to_reference_embryos/Astec-pm1.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm3.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm4.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm5.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm7.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm8.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm9.pkl']

Section astec_atlas_naming parameters provides a view on all the parameters. Most of the parameters concern the atlas building and are shared with astec_atlas (see section astec_atlas and section astec_atlas parameters).

A morphonet selection (of float type) is added to the output file that gives an estimation of the certainty (in \([0, 1]\)) of each naming.

13.3. Assessing the naming procedure on an already named embryo

If the input file is given to the testFile variable (see below), it is assumed to be already named.

testFile = 'property_file_already_named.xml'
outputFile = 'property_file_named_after_the_atlases.xml'

atlasFiles = []
atlasFiles += ['/path_to_reference_embryos/Astec-pm1.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm3.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm4.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm5.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm7.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm8.pkl']
atlasFiles += ['/path_to_reference_embryos/Astec-pm9.pkl']

Then a 64-cells time point is searched and the embryo is renamed from this given time point. Comparison between new names and actual ones are reported.

A morphonet selection (of selection type) is added to the output file where

  • 100 indicates the future naming errors (cells that will divide, whose daughter names will be switched)

  • 200 indicates the sister cells whose name has been switched

  • 255 indicates the other errors

Calling astec_atlas_naming with the -extract-selection option allows to write selection files (in the morphonet sense) together with the ouput file.