Journal Article

PUBDB-2024-05637

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data

Siggel, M.Extern* ; Jensen, R. K.Extern*EMBL* ; Maurer, V. J.CSSB* ; Mahamid, J. ; Kosinski, J. (Corresponding author)CSSB*

2024
Elsevier San Diego, Calif.

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Please use a persistent id in citations: doi:10.1016/j.jsb.2024.108067  doi:10.3204/PUBDB-2024-05637

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 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.

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Contributing Institute(s):

1. CSSB-EMBL-JK (CSSB-EMBL-JK)

Research Program(s):

1. 899 - ohne Topic (POF4-899) (POF4-899)

Experiment(s):

1. No specific instrument

Appears in the scientific report 2024

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Database coverage:
; ; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Ebsco Academic Search ; Essential Science Indicators ; IF < 5 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection ; Zoological Record

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