6. Image sequence properties

6.1. Cell unique id

Properties are computed over a temporal series of 3D images. The time point corresponding to an image is encoded into the image name by a string _t<ttt> where <ttt> are three digits. Time points may start at 0 (ie _t000), 1 (ie _t001), or later, but are a continuous series of integers.

In one 3D image, or snapshot, objects of interest (cells) are individualized by a label (ie an integer number). By convention, the background used the 1 label, and the cell labels are strictly larger than 1, but they are not necessarily a continuous series of integer numbers starting at 2.

A same label can be used in different snapshots. To differentiate cells from the different snapshots, each cell is being given an unique id, defined by \(T \times 10000 + label\), where T is the time point of the image and label the cell identifier in the image. Thus the id 100256 designates the cell of label 256 in the snapshot of time point 10.

6.2. Properties file format

The handled format are

  • pkl: a native python format. It can be used for its efficiency. Properties are stored as a python dictionary, each entry corresponding to a given property.

    The following code allows to read a pkl file. The dictionary d will contain the computed properties.

    import pickle as pkl
inputfile = open('Pm3.pkl','rb')
d = pkl.load(inputfile)
inputfile.close()

  • xml: as a text format, it can be easily parsed. Properties are enclosed in the element defined by the data tag as above.

    <data>
...
</data>

6.3. Properties

Each given property are identified by a tag in xml files, which is also the key for the same properties in the python dictionary stored in pkl files.

The command

$ astec_embryoproperties -i file.pkl --print-content

displays the properties stored in a property file. The same stands for xml files.

In pkl files, each property is also a dictionary whose keys are cell unique ids, while in xml files, each property is an element tagged by cell with the cell-id attribute.

6.3.1. Morphometric properties

Morphometric properties, computed by astec, have already been described in the dedicated astec documentation section image sequence properties

6.3.2. Ascidian dedicated properties

  • cell_name: cell name (Conklin’s nomenclature) Cell names are computed at one time point by ascidian_naming_timepoint (cf section ascidian_naming_timepoint) and propagated all over the temporal series by ascidian_naming_propagation (cf section ascidian_naming_propagation).

    <data>
  ...
  <cell_name>
    ...
    <cell cell-id="100256">'a7.0004_'</cell>

    ...
  </cell_name>
  ...
</data>

    indicates that cell labeled 256 in image of time 10 is named a7.0004_.

  • cell_fate: cell fate depends only on cell name (see section Ascidian cell fates). It is computed by ascidian_naming_propagation after all cells have been named. It can also be recomputed by ascidian_embryo (cf section ascidian_naming_propagation).

    <data>
  ...
  <cell_fate>
    ...
    <cell cell-id="100256">'Trunk Lateral Cell'</cell>

    ...
  </cell_fate>
  ...
</data>

    indicates that cell labeled 256 in image of time 10 has Trunk Lateral Cell as fate.

  • morphonet dedicated properties

    Some computed properties are dedicated for visualisation with morphonet. In xml files, such elements have a mn_type attribute (whose value is either selection or float), as in

    <data>
  ...
  <tissuefate_lemaire_2009 mn_type="selection">
    ...
    <cell cell-id="100256">[24]</cell>

    ...
  </tissuefate_lemaire_2009>
  ...
</data>

    The tissuefate_lemaire_2009 property allows to colorize cells according to their fate. ascidian_embryo allows to write a morphonet text file per morphonet property from a property file (cf section ascidian_naming_propagation).

6.3.3. Ascidian cell fates

The fates are set for a number of cells. For the other cells

  • progeny: fates are just propagated. Eg, both a7.1 and a7.2 will have Anterior Head Endoderm as fate

  • ancestors: their fates are the union of progeny fates. Eg, a6.2 has both 1st Lineage, Notochord and Posterior Ventral Neural Plate as fates.

a cells
├── a6.1 Anterior Head Endoderm
├── a6.2
│  ├── a7.3 1st Lineage, Notochord
│  └── a7.4 Posterior Ventral Neural Plate
├── a6.3
│  ├── a7.5 Anterior Head Endoderm
│  └── a7.6 Trunk Lateral Cell
├── a6.4
│  ├── a7.7 1st Lineage, Notochord
│  └── a7.8
│     ├── a8.15 Posterior Lateral Neural Plate
│     └── a8.16
│        ├── a9.31 2nd Lineage, Tail Muscle
│        └── a9.32 Posterior Lateral Neural Plate
├── a6.5 Anterior Ventral Neural Plate
├── a6.6 Head Epidermis
├── a6.7
│  ├── a7.13 Anterior Dorsal Neural Plate
│  └── a7.14 Head Epidermis
└── a6.8 Head Epidermis

b cells
├── b6.1
│  ├── b7.1 Posterior Head Endoderm
│  └── b7.2
│     ├── b8.3 Posterior Head Endoderm
│     └── b8.4 Endodermal Strand
├── b6.2
│  ├── b7.3
│  │  ├── b8.5 Mesenchyme
│  │  └── b8.6 2nd Lineage, Notochord
│  └── b7.4 1st Lineage, Tail Muscle
├── b6.3
│  ├── b7.5
│  │  ├── b8.9
│  │  │  ├── b9.17 1st Lineage, Tail Muscle
│  │  │  └── b9.18 Trunk Ventral Cell
│  │  └── b8.10
│  │     ├── b9.19 1st Lineage, Tail Muscle
│  │     └── b9.20 Trunk Ventral Cell
│  └── b7.6 Germ Line
├── b6.4
│  ├── b7.7 Mesenchyme
│  └── b7.8 1st Lineage, Tail Muscle
├── b6.5
│  ├── b7.9
│  │  ├── b8.17
│  │  │  ├── b9.33 2nd Lineage, Neural Plate
│  │  │  └── b9.34 2nd Lineage, Tail Muscle
│  │  └── b8.18 Midline Tail Epidermis
│  └── b7.10 Germ Line
│     ├── b8.19 Posterior Dorsal Neural Plate
│     └── b8.20 Midline Tail Epidermis
├── b6.6 Head Epidermis
│  ├── b7.11
│  │  ├── b8.21
│  │  │  ├── b9.41 Midline Tail Epidermis
│  │  │  └── b9.42 Medio-Lateral Tail Epidermis
│  │  └── b8.22
│  │     ├── b9.43 Medio-Lateral Tail Epidermis
│  │     └── b9.44 Lateral Tail Epidermis
│  └── b7.12
│     ├── b8.23 Medio-Lateral Tail Epidermis
│     └── b8.24
│        ├── b9.47 Lateral Tail Epidermis
│        └── b9.48 Medio-Lateral Tail Epidermis
├── b6.7
│  ├── b7.13
│  │  ├── b8.25
│  │  │  ├── b9.49 Medio-Lateral Tail Epidermis
│  │  │  └── b9.50 Lateral Tail Epidermis
│  │  └── b8.26 Lateral Tail Epidermis
│  └── b7.14
│     ├── b8.27 Midline Tail Epidermis
│     └── b8.28
│        ├── b9.55 Medio-Lateral Tail Epidermis
│        └── b9.56 Midline Tail Epidermis
└── b6.8
   ├── b7.15 Lateral Tail Epidermis
   └── b7.16
      ├── b8.31
      │  ├── b9.61 Medio-Lateral Tail Epidermis
      │  └── b9.62 Midline Tail Epidermis
      └── b8.32
         ├── b9.63 Medio-Lateral Tail Epidermis
         └── b9.64 Midline Tail Epidermis