PT  - JOURNAL ARTICLE
AU  - Abraham George Smith
AU  - Eusun Han
AU  - Jens Petersen
AU  - Niels Alvin Faircloth Olsen
AU  - Christian Giese
AU  - Miriam Athmann
AU  - Dorte Bodin Dresbøll
AU  - Kristian Thorup-Kristensen
TI  - RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation
AID  - 10.1101/2020.04.16.044461
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.04.16.044461
4099  - http://biorxiv.org/content/early/2020/04/18/2020.04.16.044461.short
4100  - http://biorxiv.org/content/early/2020/04/18/2020.04.16.044461.full
AB  - We present RootPainter, a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter facilitates both fully-automatic and semiautomatic image segmentation. We investigate the effectiveness of RootPainter using three plant image datasets, evaluating its potential for root length extraction from chicory roots in soil, biopore counting and root nodule counting from scanned roots. We also use RootPainter to compare dense annotations to corrective ones which are added during the training based on the weaknesses of the current model.Competing Interest StatementThe authors have declared no competing interest.