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A Local Thresholding Tool for Efficient Semi-automatic Labelling of Cells in Fluorescence Microscopy

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Bildverarbeitung für die Medizin 2023 (BVM 2023)

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In this work, we present a semi-automatic labelling tool for the annotation of complex cellular structures such as macrophages in fluorescence microscopy images. We present McLabel, a napari plugin that allows users to label structures of interest by simply scribbling outlines around the area of interest, using the triangle thresholding method with post-processing to identify the desired structure. Additionally, manual adaption of the threshold allows for quick and fine-grained local correction of the segmentation. The tool is evaluated in a user study with five experts, who annotated images both with and without the tool. The results show that variability in annotations between experts is reduced when the labelling tool is used and annotation time is reduced by a factor of five on average.

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  • 19 January 2024

    A correction has been published.


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Correspondence to Jonas Utz .

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© 2023 Der/die Autor(en), exklusiv lizenziert an Springer Fachmedien Wiesbaden GmbH, ein Teil von Springer Nature

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Utz, J. et al. (2023). McLabel. In: Deserno, T.M., Handels, H., Maier, A., Maier-Hein, K., Palm, C., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2023. BVM 2023. Informatik aktuell. Springer Vieweg, Wiesbaden.

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