We made a focalplane article https://focalplane.biologists.com/2022/07/04/trackmate-oneat-auto-track-correction-using-deep-lea. During the tracking of motile cells, solving the problem of linking objects between two consecutive timepoints becomes even more complicated, if the cells divide or undergo cell death. In the terms of trajectories, this means the addition of trajectory branches and terminations. However, dividing and dying cells are characteristic in their shape, and leveraging this biological information can aid the detection of cell division and death events, making cell tracking much more accurate. In this article we present our TrackMate action called TrackMate-Oneat (made by Varun Kapoor (Kapoorlabs, Paris), Mari Tolonen (University of Copenhagen, Denmark), a tool to autocorrect lineage trees by leveraging prior information about the cell events detected via a neural network such as oneat. The cell events supported in this action include mitosis and cell death, knowing the location of these events we autocorrect cell lineages using a local Jaqaman linker and also leverage the geometrical prior for angular location of daughter cells with respect to the mother cell. We detail the usage of this action along with other tools required to create the files needed for this action.
Kapoorlabs
