Crowdsourcing enables robust cell annotation for breast cancer pathology.

The tumor microenvironment (TME) contains important morphological and molecular cues that help determine prognosis and therapeutic responses. Deep learning models can assist pathologists in assessing such biomarkers. However, generating high-quality annotations for computational pathology remains a significant bottleneck due to the level of expertise and considerable time required for fine-grained labeling. In this study, we evaluate the feasibility of using non-expert crowdsourcing for cell annotation in hematoxylin and eosin (H&E) samples of breast cancer tissue. Unlike prior work, performance assessment was based on high-fidelity ground-truth labels derived from multiplexed immunofluorescence using CODEX data, allowing for accurate benchmarking of both experts and non-experts. We collected cell annotations from experts, semi-experts, and non-experts through Tilly, a gamified annotation application designed to train and engage users in identifying major cell types within the TME. Overall, our results show that non-expert crowdsourcing is a scalable and effective strategy for generating training data for the classification of major cell types in H&E images: tumor cells, lymphocytes, and fibroblasts. Moreover, combining large, crowdsourced datasets with smaller, high-quality subsets annotated using spatial proteomics may offer a practical annotation approach to develop more robust models while minimizing biases.

Authors

Publication Details

Journal
Open Access CRIS of the University of Bern
Published
2026-05-11
DOI
https://doi.org/10.48620/97670
Primary Topic
Cell Image Analysis Techniques
Type
article
Field-Weighted Citation Impact
0.00
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Crowdsourcing enables robust cell annotation for breast cancer pathology.

Marcos Da Silva Guimaraes, Joyce Sanders, Hugo M. Horlings, Sara Pires De Oliveira et al.
Open Access CRIS of the University of Bern
Cell Image Analysis Techniques
article

Crowdsourcing enables robust cell annotation for breast cancer pathology.

Marcos Da Silva Guimaraes, Joyce Sanders, Hugo M. Horlings, Sara Pires De Oliveira, Jelle ten Hoeve, Rolf Harkes, Rafael Bidarra, Pascal Klöckner, Siamak Hajizadeh, Sybren Lodewijk Meijer, Ibrahim Aloglu, Melis Erdal Cesur, Zainab Ameziane, Idris Iritas, Laurens Pels, Bart de Rooij
article en

Abstract

The tumor microenvironment (TME) contains important morphological and molecular cues that help determine prognosis and therapeutic responses. Deep learning models can assist pathologists in assessing such biomarkers. However, generating high-quality annotations for computational pathology remains a significant bottleneck due to the level of expertise and considerable time required for fine-grained labeling. In this study, we evaluate the feasibility of using non-expert crowdsourcing for cell annotation in hematoxylin and eosin (H&E) samples of breast cancer tissue. Unlike prior work, performance assessment was based on high-fidelity ground-truth labels derived from multiplexed immunofluorescence using CODEX data, allowing for accurate benchmarking of both experts and non-experts. We collected cell annotations from experts, semi-experts, and non-experts through Tilly, a gamified annotation application designed to train and engage users in identifying major cell types within the TME. Overall, our results show that non-expert crowdsourcing is a scalable and effective strategy for generating training data for the classification of major cell types in H&E images: tumor cells, lymphocytes, and fibroblasts. Moreover, combining large, crowdsourced datasets with smaller, high-quality subsets annotated using spatial proteomics may offer a practical annotation approach to develop more robust models while minimizing biases.

Open Access CRIS of the University of Bern
Good health and well-being
Openalex Percentile: Top 4%
Cell Image Analysis Techniques
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.