4. ascidian_naming_timepoint

ascidian_naming_timepoint can be used to name one time point of an ascidian embryo (for which the lineage and the contact surfaces are known), by name transfer from a database of named embryos (atlases).

The targeted time point is chosen by its cell count (variable cell_number). Thus, it is more convenient to choose a stage for which the cell composition is the same among all embryos (ie the 64-, 76- or 112-cells).

Then, each atlas (at the same targeted cell count) is co-registered with the embryo to be named, and cells of the atlas are paired with the ones of the unnamed embryos, yielding name candidates. Cells are paired when, after registration, their centers of mass are the closest to each other. It may then happen that some cells are not paired.

If several atlases are given, each unnamed cell may have a list of candidate names. An iterative voting procedure aloows then to propose names for the unnamed embryo.

Section Naming timepoint parameters provides a view on all the parameters.

4.1. ascidian_naming_timepoint additional options

The following options are available:

-write-selection, --write-selection

write out morphonet selection files.

4.2. 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'

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

cell_number = 64

Section Naming timepoint parameters provides a view on all the parameters.

4.3. Initial naming: parameter file examples

4.3.1. Use of transformation_filename

Most of the computation time is spend in co-registering embryos, thus in transformation computation.

When adding progressively the atlases in atlasEmbryos, or when selecting retrospectively only some atlases, it is desirable not to recompute at every experiment all the transformations. The transformation_filename variable allows to specify a file name (pickle format) where they can be saved for further re-use.

This first parameter file will name the embryo summarized in 'property_file_partially_named.xml' with the two atlases 'Astec-pm1.pkl' and 'Astec-pm3.pkl'. Computed transformations will be saved in file 'trsf.pkl'.

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

atlasEmbryos = []
atlasEmbryos += ['/path_to_reference_embryos/Astec-pm1.pkl']
atlasEmbryos += ['/path_to_reference_embryos/Astec-pm3.pkl']

transformation_filename = 'trsf.pkl'

cell_number = 64

In this second parameter file, atlases are enriched with new exemplars. Since we provided the already omputed transformations in transformation_filename, co-registrations with 'Astec-pm1.pkl' and 'Astec-pm3.pkl' will not be re-calculated. In addition, 'trsf.pkl' will be updated and will contain all co-registration transformations.

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

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

transformation_filename = 'trsf.pkl'

cell_number = 64

4.4. Initial naming: Morphonet dedicated generated field

Generated morphonet dedicated properties (in the property file) are

  • init_naming_neighborhood_assessment (mn_type is “float”)

  • init_naming_neighborhood_assessment_quality (mn_type is “float”)