Label-free droplet image analysis with Cellprofiler

Kacsor, D.; Saar-Abroi, M.; Olman, T.; Bartkova, S.; Scheler, O.

doi:10.1101/2025.04.04.647160

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bioRxiv · 10.1101/2025.04.04.647160

Label-free droplet image analysis with Cellprofiler

Kacsor, D.·Saar-Abroi, M.·Olman, T.·Bartkova, S.·Scheler, O.

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Abstract

Droplet microfluidic methods used for microbiological experiments are fast, cost-effective, and provide high-throughput data. However, analysis of such image data can be difficult, and detection of molecular labels is limited by microscope parameters. Currently, there is lack of user-friendly methods to analyse a large volume of label-free droplet images without the need for trained personnel, or expensive, proprietary software. Such methods would make droplet microfluidic technology more widely accessible for a larger range of biological applications. In this paper we demonstrate an image analysis pipeline designed using Cellprofiler, a free, open-source software. This pipeline identifies water-in-oil microfluidic droplets, microplastic particles, and bacterial growth without using fluorescent or other labels.

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Kacsor, D., Saar-Abroi, M., Olman, T., Bartkova, S., Scheler, O.. 2025-04-10. Label-free droplet image analysis with Cellprofiler. https://doi.org/10.1101/2025.04.04.647160

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