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bioRxiv · 10.1101/2023.07.04.547645

ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data

Siggel, M.·Jensen, R. K.·Mahamid, J.·Kosinski, J.
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Abstract

Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular resolution. To enable quantitative analysis of the complex shapes and morphologies of lipid membranes, the noisy three-dimensional (3D) volumes must be segmented. Despite recent advances, this task often requires considerable user intervention to curate the resulting seg-mentations. Here, we present ColabSeg, a Python-based tool for processing, visualizing, cleaning, and fitting membrane segmentations from cryo-ET data for downstream analysis. ColabSeg makes many well-established algorithms for point-cloud processing easily available to the broad community of structural biologists for applications in cryo-ET through its graphical user interface (GUI). We demonstrate the usefulness of the tool with a range of use cases and biological examples. Finally, for a large Mycoplasma pneumoniae dataset of 50 tomograms, we show how ColabSeg enables high-throughput membrane segmentation, which can be used as valuable training dataset for fully automated convolutional neural network (CNN)-based segmentation.

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Siggel, M., Jensen, R. K., Mahamid, J., Kosinski, J.. 2023-07-04. ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data. https://doi.org/10.1101/2023.07.04.547645

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