Validate lineage.json data

vanvalenlab / deepcell-tracking

Track cells and build cell lineages

Other

27 stars 6 forks source link

Validate lineage.json data #51

Open willgraf opened 3 years ago

willgraf commented 3 years ago

There should be an easy way to validate that the cell lineage data in lineage.json is valid, including (but not limited to):

Parent cell's cannot be in the last frame
A cell cannot be in a frame after it has divided or died.
A cell cannot be in the same frame as its parents or daughters.

A simple function that just makes assertions on a .trk file or a lineage.json file and informs the user of any data violations would be sufficient.

Originally posted by @willgraf in https://github.com/vanvalenlab/deepcell-tf/issues/151#issuecomment-786889143

willgraf commented 3 years ago

@MekWarrior has provided some helpful comments on lineage validation here.

MekWarrior commented 3 years ago

This issue has cropped up again and caused DCL to crash. Differences in how underlying images are stored (i.e. int64) or missing data fields could cause downstream errors if assumptions aren't met. Theses assumptions should asserted on the save functions in utils

willgraf commented 3 years ago

This is largely resolved by the is_valid_lineage changes in #73.

We may want to take the next step and integrate is_valid_lineage in load_trks and save_trks and at least warn the user on bad batches.

Ciro1990 commented 2 years ago

Is there a way to visualize/build lineage trees from the tracks? something similar to Arboretum plugin for napari for example