gronteix/cell-tracking-2d

What is it

Analysis of OT1 behavior on spheroid analysis. The different Notebooks compile approaches.

Creating the datasets to analyze

To classify the presence of the T cells on the spheroid, we use the FindApheroidNotebook.

Most of the computations are run on variants of this original core dataframe. In order to compute these variations we use the CreatingData Notebook.

OT1 motility

To study the dynamics wrt the spheroid, we use the OT1onSpheroid Notebook. The global cell motility dynamics (MSD...) is obtained through the DataAnalysis notebook.

OT1 behavior once in contact

In order to infer chemotaxis, we can look at the distribution of T-cells on the spheroid surface. The study of these could give hints on the randomness of the accumulation rate.

Inferring spheroid death

We infer the causes of spheroid death from the comparisonFrame notebook.

Notes

All legacy code stored in "legacy" folder.