ArticleProtein science : a publication of the Protein Society2021
High resolution electron tomography and segmentation-by-modeling interpretation in Bsoft.
Article in Protein science : a publication of the Protein Society, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 14 citations in OpenAlex.
- AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput.Nature methods · 2026Article
- Review
- A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries.Current opinion in structural biology · 2025Review
- An approach for coherent periodogram averaging of tilt-series data for improved contrast transfer function estimation.FEBS open bio · 2025Article
- Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data.Journal of molecular biology · 2023Review
- Bsoft: Image Processing for Structural Biology.Bio-protocol · 2022Article
- Nanoscale architecture of a VAP-A-OSBP tethering complex at membrane contact sites.Nature communications · 2021Article
- Article
- High resolution electron tomography and segmentation-by-modeling interpretation in Bsoft.Protein science : a publication of the Protein Society · 2021Article
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1 author at 1 institution in 1 country.
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Abstract
Bsoft offers many tools for the processing of tomographic tilt series and the interpretation of tomograms. Since I introduced tomography into Bsoft almost two decades ago, the field has advanced significantly, requiring refinement of old algorithms and development of new ones. The current direct detectors allow us to collect data more efficiently and with better quality, progressing towards automation. The goal is then to also automate alignment of tilt series and reconstruction. I added an estimation of the specimen thickness as well as fiducialless alignment, to augment the existing fiducial-based alignment. High-resolution work requires correction for the contrast transfer function, in tomography complicated by the tilted specimen. For this, I developed a method to generate a power spectrum using the whole micrograph, compensating for tilting. This is followed by routine determination of the contrast transfer function, and correction for it during reconstruction. The next steps involve interpretation of the tomogram, either by subtomogram averaging where possible, or by segmentation and modeling otherwise. Such interpretation actually constitutes the main time-consuming part of tomography and is less amenable to automation compared to the initial reconstruction.
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