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

2024; Elsevier BV; Volume: 216; Issue: 2 Linguagem: Inglês

10.1016/j.jsb.2024.108067

1095-8657

Marc Siggel, Rasmus K. Jensen, Valentin Maurer, Julia Mahamid, Jan Kosiński,

Advanced Fluorescence Microscopy Techniques

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 segmentations. Here, we present ColabSeg, a Python-based tool for processing, visualizing, editing, 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 data for fully automated convolutional neural network (CNN)-based segmentation.