9. Gallery¶
9.1. Temporal alignment of cell count¶
The temporal alignment of total cell count can be assessed by
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['cell-count-wrt-time']
It generates a python
file allowing to generate the following figure.
9.2. Temporal alignment of epidermis cell count¶
The temporal alignment of cell (having an epidermis fate) count can be assessed by
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['epidermis-cell-count-wrt-time']
It generates a python
file allowing to generate the following figures.
9.3. Temporal cell composition variability¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['name-composition-wrt-time']
It generates a python
file allowing to generate the following figures.
9.4. Embryo volume variation¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['embryo-volume']
It generates a python
file allowing to generate the following figures.
9.5. Cell neighbor count¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['neighbors-wrt-cell-number']
It generates a python
file allowing to generate the following figures.
9.6. Embryo symmetry axis¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['leftright-symmetry-axis']
It generates a python
file allowing to generate the following figures.
9.7. Time interval of cell division¶
Measures the time interval length for a given cell (a cell of given name). Intra-embryo measure is obtained by comparing left and right hemispheres.
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['division-timeinterval']
It generates a python
file allowing to generate the following figures.
9.8. Ordering of cell division¶
Measures the time interval length for a given cell (a cell of given name). Intra-embryo measure is obtained by comparing left and right hemispheres.
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['division-order']
It generates a python
file allowing to generate the following figures (among others).
9.9. Cell-to-cell distance along branches¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['cell-distance-along-branch']
It generates a python
file allowing to generate the following figures.
9.10. Cell-to-cell distances¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['cell-distance-histograms']
It generates a python
file allowing to generate the following figures.
9.11. Division-to-division distances¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['division-distance-histograms']
It generates a python
file allowing to generate the following figures.
9.12. Division dendrograms¶
ascidian_atlas -p parameters-atlas.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['division-dendrograms']
It generates a python
file allowing to generate division dendrograms, plus asome additional figures.
The command
python figures_division_dendrogram.py
will generate dendrograms for all divisions, which may be pretty long. Alternatively, dendrograms for chosen divisions may be generated by giving cell names as arguments as in
python figures_division_dendrogram.py 'b7.0002_' 'a7.0002_'
There are four figures generated by division, here are the ones for the division of cell 'b7.0002_'
:
'b7_0002U_HC028_BAL008_single.png'
: dendrograms of cell divisions, the cost function being the division-to-dision distance.b7_0002U
represents the cell name (U
stands for_
(ie right cells),S
for*
()ie left cells) In the dendrogram, embryos prefixed by'sym-'
designated the symmetric cell (cell from the other hemisphere)'b7_0002U_HC028_BAL008_single_v2_SW.png'
: id as'b7_0002U_HC028_BAL008_single.png'
but with additional (fake) divisions are added, where the daughter names are switched (prefixed by switched). It allows to assess whether daughter name couples are consistent.'HC028_b7_0002U_single_v2.png'
: id as'b7_0002U_HC028_BAL008_single.png'
, only the name has changed. The prefix'HC028'
indicates the highest value of the dendrogram (the higher, the more likely there are several division geometry modes).'HC028_b7_0002U_single_v2_SW.png'
: id as'b7_0002U_HC028_BAL008_single_v2_SW.png'
In addition, to the cell division dendrograms, some other figures are generated
9.13. Leave-one-out tests for initial naming by registration (wrt atlas count)¶
Leave-one-out tests for initial naming by registration, for embryos chosen at a given cell count.
ascidian_atlas_init_naming -p parameters-atlas-init.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl']
generate_figure = ['atlas-naming-register-leave-one-out-wrt-atlases']
cell_number = 64
direction_sample = 'symmetric-cell'
symmetric_cell_similarity = 'winged-contact'
transformation_filename = 'trsf64'
It generates a python
file allowing to generate the following figures.
9.14. Leave-one-out tests for initial naming by registration (wrt cell count)¶
Leave-one-out tests for initial naming by registration, for embryos chosen at a given cell count, and different atlases count.
ascidian_atlas_init_naming -p parameters-atlas-init.py
with the following parameter file
atlasFiles = ['Pm1.pkl', 'Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl', 'Pm9.pkl']
generate_figure = ['atlas-naming-register-leave-one-out-wrt-cells']
cell_number = 64
direction_sample = 'symmetric-cell'
symmetric_cell_similarity = 'winged-contact'
transformation_filename = 'trsf64'
It generates a python
file allowing to generate the following figures.
It generates a python
file allowing to generate the following figures.
9.15. Division-to-division distances used to named the unnamed embryo¶
Leave-one-out tests for initial naming by registration, for embryos chosen at a given cell count, and different atlases count.
ascidian_atlas_naming -p parameters-atlas-naming.py
with the following parameter file
atlasFiles = ['Pm3.pkl'. 'Pm4.pkl', 'Pm5.pkl', 'Pm7.pkl', 'Pm8.pkl']
testFile = 'Pm1.pkl'
generate_figure = ['atlas-naming-distance']
cell_number = 64
direction_sample = 'symmetric-cell'
symmetric_cell_similarity = 'winged-contact'
It generates a python
file allowing to generate the following figures.