TITLE: NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation 

ABSTRACT: High-resolution mapping of cells and tissue structures provides a foundation
for developing interpretable machine-learning models for computational
pathology. Deep learning algorithms can provide accurate mappings given large
numbers of labeled instances for training and validation. Generating adequate
volume of quality labels has emerged as a critical barrier in computational
pathology given the time and effort required from pathologists. In this paper
we describe an approach for engaging crowds of medical students and
pathologists that was used to produce a dataset of over 220,000 annotations of
cell nuclei in breast cancers. We show how suggested annotations generated by a
weak algorithm can improve the accuracy of annotations generated by non-experts
and can yield useful data for training segmentation algorithms without
laborious manual tracing. We systematically examine interrater agreement and
describe modifications to the MaskRCNN model to improve cell mapping. We also
describe a technique we call Decision Tree Approximation of Learned Embeddings
(DTALE) that leverages nucleus segmentations and morphologic features to
improve the transparency of nucleus classification models. The annotation data
produced in this study are freely available for algorithm development and
benchmarking at: https://sites.google.com/view/nucls.
High-resolution mapping of cells and tissue structures provides a foundation
for developing interpretable machine-learning models for computational
pathology. Deep learning algorithms can provide accurate mappings given large
numbers of labeled instances for training and validation. Generating adequate
volume of quality labels has emerged as a critical barrier in computational
pathology given the time and effort required from pathologists. In this paper
we describe an approach for engaging crowds of medical students and
pathologists that was used to produce a dataset of over 220,000 annotations of
cell nuclei in breast cancers. We show how suggested annotations generated by a
weak algorithm can improve the accuracy of annotations generated by non-experts
and can yield useful data for training segmentation algorithms without
laborious manual tracing. We systematically examine interrater agreement and
describe modifications to the MaskRCNN model to improve cell mapping. We also
describe a technique we call Decision Tree Approximation of Learned Embeddings
(DTALE) that leverages nucleus segmentations and morphologic features to
improve the transparency of nucleus classification models. The annotation data
produced in this study are freely available for algorithm development and
benchmarking at: https://sites.google.com/view/nucls.
NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation
http://arxiv.org/abs/2102.09099v1