Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS Article Swipe
Robert Kiewisz
,
Gunar Fabig
,
William F. Conway
,
Jake Johnston
,
V.A. Kostyuchenko
,
Cyril Bařinka
,
Oliver B. Clarke
,
Magdalena M. Magaj
,
Hossein Yazdkhasti
,
Francesca Vallese
,
Shee‐Mei Lok
,
Stefanie Redemann
,
Thomas Müller‐Reichert
,
Tristan Bepler
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.12.19.629196
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.12.19.629196
Segmentation of macromolecular structures is the primary bottleneck for studying biomolecules and their organization with electron microscopy in 2D/3D – requiring months of manual effort. Transformer-based Rapid Dimensionless Instance Segmentation (TARDIS) is a deep learning framework that automatically and accurately annotates membranes and filaments. Pre-trained TARDIS models can segment electron tomography (ET) reconstructions from both 3D and 2D electron micrographs of cryo and plastic-embedded samples. Furthermore, by implementing a novel geometric transformer architecture, TARDIS is the only method to provide accurate instance segmentations of these structures. Reducing the annotation time for ET data from months to minutes, we demonstrate segmentation of membranes and filaments in over 13,000 tomograms in the CZII Data Portal. TARDIS thus enables quantitative biophysical analysis at scale for the first time. We show this in application to kinetochore-microtubule attachment and viral-membrane interactions. TARDIS can be extended to new biomolecules and applications and open-source at https://github.com/SMLC-NYSBC/TARDIS .
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.12.19.629196
- OA Status
- green
- Cited By
- 10
- References
- 68
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4405631312
All OpenAlex metadata
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https://doi.org/10.1101/2024.12.19.629196Digital Object Identifier
- Title
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Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDISWork title
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preprintOpenAlex work type
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enPrimary language
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2024Year of publication
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2024-12-20Full publication date if available
- Authors
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Robert Kiewisz, Gunar Fabig, William F. Conway, Jake Johnston, V.A. Kostyuchenko, Cyril Bařinka, Oliver B. Clarke, Magdalena M. Magaj, Hossein Yazdkhasti, Francesca Vallese, Shee‐Mei Lok, Stefanie Redemann, Thomas Müller‐Reichert, Tristan BeplerList of authors in order
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://doi.org/10.1101/2024.12.19.629196Direct OA link when available
- Concepts
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Materials science, Membrane, Segmentation, Artificial intelligence, Computer science, Chemistry, BiochemistryTop concepts (fields/topics) attached by OpenAlex
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2025: 9, 2024: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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