delta.lineage.Lineage¶

class delta.lineage.Lineage(cells=<factory>)[source]¶

Represents the cell lineages contained in a ROI.

Only two functions are required to create a full lineage tree:

create and extend to create a cell and extend it frame after frame;

               create(frame=0)
                ------------>
frames : 0....5....        0....5....
cell #1:                   ╺

               create(frame=5)
                ------------>
frames : 0....5....        0....5....
cell #1: ╺╼╼╼╼╼╼╼╼╼        ╺╼╼╼╼╼╼╼╼╼
cell #2:                        ╺

         create(frame=5, motherid=1)
                ------------>
frames : 0....5....        0....5....
cell #1: ╺╼╼╼╼╼╼╼╼╼        ╺╼╼╼╼┮╼╼╼╼
cell #2:                        ┕

               extend(cellid=2)
                ------------>
frames : 0....5....        0....5....
cell #1: ╺╼╼╼╼┮╼╼╼╼        ╺╼╼╼╼┮╼╼╼╼
cell #2:      ┕                 ┕╼

To manipulate an already created tree, one needs four more:

split and merge, to split a cell into two cells, and reverse the operation;
adopt, to change the mother of a cell;
pivot, to switch the roles of mother and daughter cells.

The use of these methods is best illustrated by the following diagrams:

              split(1, frame=5)
                ------------>
frames : 0....5....        0....5....
cell #1: ╺╼╼╼╼╼╼╼╼╼        ╺╼╼╼╼
cell #2:                        ╺╼╼╼╼
                <------------
                 merge(2, 1)

                 adopt(2, 1)        pivot(2)        adopt(2, None)
                ------------>     ------------>     ------------->
frames : 0..3......        0..3......        0..3......        0..3......
cell #1: ╺╼╼╼╼╼╼╼╼╼        ╺╼╼┮╼╼╼╼╼╼        ╺╼╼┮╼╼╼           ╺╼╼╼╼╼╼
cell #2:    ╺╼╼╼              ┕╼╼╼              ┕╼╼╼╼╼╼           ╺╼╼╼╼╼╼
                <------------     <------------     <-------------
                adopt(2, None)       pivot(2)         adopt(2, 1)

__init__(cells=<factory>)[source]¶

Methods

`__init__`([cells])
`adopt`(cellid, motherid)	Attribute a new mother `motherid` (which can be `None`) to the cell `cellid`.
`compare`(other[, level])	Print or return the list of differences between two Lineage objects.
`compute_growthrates`(feature[, smooth_frames])	Compute the growth rates of all cells on all frames and store them.
`create`(frame, features[, motherid])	Create a new cell at frame `frame`.
`extend`(cellid, features)	Extend `cellid` with one more frame.
`merge`(cellid, merge_into_cellid)	Rename a cell (`cellid`) to merge it into another one (`merge_into_cellid`).
`pivot`(cellid)	Swap the roles between cell `cellid` and its mother.
`split`(cellid, frame)	Break a cell lineage into two independent cell lineages.
`swap_poles`(cellid[, frame])	Swap the poles of the cell `cellid` for all the frames or for frame `frame` onwards.

Attributes

cells

Dictionary of cellids to ``Cell``s