PT  - JOURNAL ARTICLE
AU  - Miroslav Poláček
AU  - Alexis Arizpe
AU  - Patrick Hüther
AU  - Lisa Weidlich
AU  - Sonja Steindl
AU  - Kelly Swarts
TI  - Automation of tree-ring detection and measurements using deep learning
AID  - 10.1101/2022.01.10.475709
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.10.475709
4099  - http://biorxiv.org/content/early/2022/01/12/2022.01.10.475709.short
4100  - http://biorxiv.org/content/early/2022/01/12/2022.01.10.475709.full
AB  - We present an implementable neural network-based automated detection and measurement of tree-ring boundaries from coniferous species.We trained our Mask R-CNN extensively on over 8,000 manually annotated rings. We assessed the performance of the trained model from our core processing pipeline on real world data.The CNN performed well, recognizing over 99% of ring boundaries (precision) and a recall value of 95% when tested on real world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were a 99% match with human measurements of the same samples.Our CNN is readily deployable through a Docker container and requires only basic command line skills. Application outputs include editable annotations which facilitate the efficient generation of ring-width measurements from tree-ring samples, an important source of environmental data.Competing Interest StatementThe authors have declared no competing interest.