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DeepMuCS: A Framework for Co-culture Microscopic Image Analysis: From Generation to Segmentation

Nabeel Khalid; Mohammadmahdi Koochali; Vikas Rajashekar; Mohsin Munir; Christoffer Edlund; Rickard Sjögren; Andreas Dengel; Sheraz Ahmed
In: 2022 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI). IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI-2022), September 27-30, Ioannina, Greece, IEEE BHI-BSN 2022, 2022.


Discrimination between cell types in the co-culture environment with multiple cell lines can assist in examining the interaction between different cell populations. Identifying different cell cultures in addition to cell segmentation in co-culture is essential for understanding the cellular mechanisms associated with disease states. In drug development, biologists are more interested in co-culture models because they replicate the tumor environment in vivo better than the monoculture models. Additionally, they have a measurable effect on cancer cell response to treatment. Co-culture models are critical for designing a drug with maximum efficacy on cancer while minimizing harm to the rest of the body. In the past, there existed minimal progress related to cell-type aware segmentation in the monoculture and no development whatsoever for the co-culture. The introduction of the LIVECell dataset has allowed us to perform experiments for cell-type-aware segmentation. However, it is composed of microscopic images in a monoculture environment. This paper presents a framework for co-culture microscopic image data generation, where each image can contain multiple cell cultures. The framework also presents a pipeline for culture-dependent cell segmentation in co-culture microscopic images. The extensive evaluation revealed that it is possible to achieve cell-type aware segmentation in co-culture microscopic images with good precision.