Publication

DeepCIS: An end-to-end Pipeline for Cell-type aware Instance Segmentation in Microscopic Images

Nabeel Khalid, Mohsin Munir, Christoffer Edlund, Timothy R Jackson, Johan Tryggy, Rickard Sjögren, Andreas Dengel, Sheraz Ahmed

In: IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS (BHI’21) JOINTLY ORGANISED WITH THE 17TH IEEE-EMBS INTERNATIONAL CONFERENCE ON WEARABLE AND IMPLANTABLE BODY SENSOR NETWORKS (BSN’21). IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI-2021) July 27-30 Athens Europe Greece ISBN 978-1-6654-4770-6 IEEE 8/2021.

Abstract

Accurate cell segmentation in microscopic images is a useful tool to analyze individual cell behavior, which helps to diagnose human diseases and development of new treatments. Cell segmentation of individual cells in a microscopic image with many cells in view allows quantification of single cellular features, such as shape or movement patterns, providing rich insight into cellular heterogeneity. Most of the cell segmentation algorithms up till now focus on segmenting cells in the images without classifying the culture of the cell in the images. Discrimination among cell types in microscopic images can lead to a new era of high-throughput cell microscopy. Multiple cell types in coculture can be easily identified and studying the changes in cell morphology can lead to many applications such as drug treatment. To address this gap, DeepCIS is proposed to detect, segment, and classify the culture of the cells and nucleus in the microscopic images. We have used the EVICAN60 dataset which contains microscopic images from a variety of microscopes having numerous cell cultures, to evaluate the proposed pipeline. To further demonstrate the utility of the DeepCIS, we have designed various experimental settings to uncover its learning potential. We have achieved a mean average precision score of 24.37% for the segmentation task averaged over 30 classes for cell and nucleus.

Projekte

DeepCIS.pdf (pdf, 2 MB )

German Research Center for Artificial Intelligence
Deutsches Forschungszentrum für Künstliche Intelligenz