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: evaluation

Evaluation of the naming propagation can be done by the means of three measures, that can be exported as morphonet properties for visualisation purposes (see ascidian_embryo). In xml files, such elements have a mn_type attribute (whose value is either group, float, or label, see morphonet formats).

  • naming_score (mn_type='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). Only a subset of the atlases are retained to account for potential different division directions, and then only consider atlases where the assessed division divides along the same direction.

    \(n\) 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)

    Important

    The naming score is computed independently (and retrospectively) from the naming procedure: it is therefore evaluated for every division detected in the reconstruction for which at least one exemplar exists in the atlases, even for divisions named by other means: names assigned manually, or derived from the initial naming procedure (embryo alignment).

  • naming_agreement (mn_type='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 expected to be in \([0.5, 1]\). A value of 1 means that all atlases agree.

    Important

    Some cells may not have a naming_agreement value. Either, they are not named, or they are named by back-propagation. E.g. the initial naming is done at, say, a timepoint of the 64 cell stage. Cells before this timepoint are straightforwrd named, but do not receive a naming_agreement value.

  • naming_unequal_division_flag (mn_type='label')

    The unequal divisions are the divisions where the volume of one daughter cell is always larger than the one of its sister, for all of the atlases. Divisions (ie mother cells), identified as unequal divisions from the atlases, for which the cell volume ordering differs in the named embryo (with respect to the atlases) are labeled by 255.

5.4. Naming propagation: evaluation 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 as a morphonet property for visualisation purposes (see ascidian_embryo).

  • renaming_flag (mn_type='label')

    • 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