12. astec_atlas_init_naming

astec_atlas_init_naming can be used to name one time point of an ascidian embryo (for which the lineage and the contact surfaces are known).

Section astec_atlas_init_naming parameters provides a view on all the parameters.

12.1. astec_atlas_init_naming additional options

The following options are available:

-write-selection, --write-selection

write out morphonet selection files

12.2. Initial naming of an embryo

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

  • the input property file, containing the lineage, the contact surfaces, and the volumes.

  • the output property file,

  • the list of atlases (already named embryos),

  • the cell number of the time point to be named (typically 64 or 112)

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']

cell_number = 64

Section astec_atlas_init_naming parameters provides a view on all the parameters.