Danita C, Chiu W, Galaz-Montoya JG. Efficient manual annotation of cryogenic electron tomograms using IMOD.
STAR Protoc 2022;
3:101658. [PMID:
36097385 PMCID:
PMC9463458 DOI:
10.1016/j.xpro.2022.101658]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/28/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
Annotation highlights and segmentation isolates features in cryogenic electron tomograms to improve visualization and quantification of features (for example, their size and abundance, and spatial relationships with other features), facilitating phenotypic structural analyses of cellular tomograms. Here, we present a manual annotation protocol using the open-source software IMOD and describe segmentation of three types of common cellular features: membranes, large globules, and filaments. IMOD’s interpolation function can improve the speed of manual annotation up to an order of magnitude.
Interpolation between sparsely annotated slices speeds up manual annotation
Manual annotation differentiates between similar features in different contexts
Turning annotations into segmentations shows actual data instead of representations of it
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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