5. ascidian_naming_propagation

ascidian_naming_propagation 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 Naming propagation parameters provides a view on all the parameters.

5.1. ascidian_naming_propagation additional options

The following options are available:

-write-selection, --write-selection

write out morphonet selection files

5.2. 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'

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']

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

5.3. Naming propagation: Morphonet dedicated generated field

Generated morphonet dedicated properties (in the property file) are

• name_choice_agreement (mn_type is “float”)

  Gives the fraction of atlases that agrees with the name choice. E.g. a value of \(0.8888\) (equal to \(8/9\)) indicates that 8 atlases out of 9 were giving that particular choice. As a consequence, since the most probable choice is ever made, values are in \([0.5, 1[\). When all atlases agree (meaning a fraction of \(1.0\)) the property is not filled. Thus only the cells issued from a division named with a partial agreement have a value.

• name_choice_score.txt (mn_type is “float”)

  Gives the score average of the \(n\) closest atlases to the naming choice. An atlas score (in \([0, 1]\)) is equal to \(1.0\) minus the normalized distance between the vector of contact surfaces of the two daughter cells of the embryo to be named and the same vector of an atlas (\(0\) means minimal distance or perfect agrement; \(1\) is complete disagreement, and conversely for the score).

  \(n\) is computed by \(n = \max( n_{min} , c * n_{atlases} / 100.0 )\) where

  • \(c\) is a the percentage of atlases to be retained (parameter confidence_atlases_percentage, section 7.6). It allows to discard atlases that give large distances (eg in case of multiple division directions)

  • \(n_{min}\) is the minimal number of atlases (parameter confidence_atlases_nmin, section 7.6) to be used for the average (if \(0\), all the \(n = c * n_{atlases} / 100.0\) are kept).

  • confidence_atlases_percentage = 50 and confidence_atlases_nmin=2 means that the average is computed on half of the atlases (if there are more than 4 atlases exhibiting the sought division or at least 2 atlases)

5.4. 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'

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']

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