Skip to Main content Skip to Navigation
New interface
Journal articles

Tracking cell lineages in 3D by incremental deep learning

Abstract : Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently lack a unified user interface. We present ELEPHANT, an interactive platform for 3D cell tracking that addresses these challenges by taking an incremental approach to deep learning. ELEPHANT provides an interface that seamlessly integrates cell track annotation, deep learning, prediction, and proofreading. This enables users to implement cycles of incremental learning starting from a few annotated nuclei. Successive prediction-validation cycles enrich the training data, leading to rapid improvements in tracking performance. We test the software's performance against state-of-the-art methods and track lineages spanning the entire course of leg regeneration in a crustacean over 1 week (504 timepoints). ELEPHANT yields accurate, fully-validated cell lineages with a modest investment in time and effort.
Document type :
Journal articles
Complete list of metadata

https://hal-cnrs.archives-ouvertes.fr/hal-03799482
Contributor : Michalis Averof Connect in order to contact the contributor
Submitted on : Wednesday, October 5, 2022 - 10:25:43 PM
Last modification on : Saturday, October 8, 2022 - 3:52:33 AM

File

elife-69380-v1.pdf
Publisher files allowed on an open archive

Identifiers

Collections

Citation

Ko Sugawara, Çağrı Çevrim, Michalis Averof. Tracking cell lineages in 3D by incremental deep learning. eLife, 2022, 11, ⟨10.7554/elife.69380⟩. ⟨hal-03799482⟩

Share

Metrics

Record views

3

Files downloads

2