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A CTF-Based Data Augmentation Method for the Segmentation of Lipid Nanoparticles in Cryo-EM
Lipid nanoparticles (LNPs) were prepared as described (https://doi.org/10.1038/s42003-021-02441-2) using the lipids DLin-KC2-DMA, DSPC, cholesterol, and PEG-DMG2000 at mol ratios of 50:10:38.5:1.5. RNA was not included and LNPs were ejected into pH 4 and pH 7.4 buffer after microfluidic assembly. To prepare samples for imaging, 3 μL of LNP formulation was applied to holey carbon grids (Quantifoil, R3.5/1, 200 mesh copper). Grids were then incubated for 30 s at 298 K and 100% humidity before blotting and plunge-freezing into liquid ethane using a Vitrobot Mark IV (Thermo Fisher Scientific). Grids were imaged at 200 kV using a Talos Arctica system equipped with a Falcon 3EC detector (Thermo Fisher Scientific). A nominal magnification of 45,000x was used, corresponding to images with a pixel count of 4096x4096 and a calibrated pixel spacing of 0.223 nm. Micrographs were collected as dose-fractionated "movies" at nominal defocus values between -1 and -3 μm, with 10 s total exposures consisting of 66 frames with a total electron dose of 12,000 electrons per square nanometer. Movies were motion-corrected using MotionCor2 (https://doi.org/10.1038/nmeth.4193), resulting in flattened micrographs suitable for downstream particle segmentation. Images were manually segmented into particle and non-particle regions. Segmentation masks and their corresponding images are deposited in this data set.
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "006:55" ] |
| contactPoint |
{ "fn": "Thomas Cleveland", "hasEmail": "mailto:thomas.cleveland@nist.gov" } |
| description | Lipid nanoparticles (LNPs) were prepared as described (https://doi.org/10.1038/s42003-021-02441-2) using the lipids DLin-KC2-DMA, DSPC, cholesterol, and PEG-DMG2000 at mol ratios of 50:10:38.5:1.5. RNA was not included and LNPs were ejected into pH 4 and pH 7.4 buffer after microfluidic assembly. To prepare samples for imaging, 3 μL of LNP formulation was applied to holey carbon grids (Quantifoil, R3.5/1, 200 mesh copper). Grids were then incubated for 30 s at 298 K and 100% humidity before blotting and plunge-freezing into liquid ethane using a Vitrobot Mark IV (Thermo Fisher Scientific). Grids were imaged at 200 kV using a Talos Arctica system equipped with a Falcon 3EC detector (Thermo Fisher Scientific). A nominal magnification of 45,000x was used, corresponding to images with a pixel count of 4096x4096 and a calibrated pixel spacing of 0.223 nm. Micrographs were collected as dose-fractionated "movies" at nominal defocus values between -1 and -3 μm, with 10 s total exposures consisting of 66 frames with a total electron dose of 12,000 electrons per square nanometer. Movies were motion-corrected using MotionCor2 (https://doi.org/10.1038/nmeth.4193), resulting in flattened micrographs suitable for downstream particle segmentation. Images were manually segmented into particle and non-particle regions. Segmentation masks and their corresponding images are deposited in this data set. |
| distribution |
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| identifier | ark:/88434/mds2-4063 |
| issued | 2026-03-30 |
| keyword |
[ "AI", "CTF", "Contrast transfer function", "Cryo-EM", "Drug delivery", "KC2", "LNP", "Lipid", "ML", "TEM", "augmentation", "electron microscopy", "machine learning", "nanoparticle", "segmentation" ] |
| language |
[ "en" ] |
| license | https://www.nist.gov/open/license |
| modified | 2026-02-23 00:00:00 |
| programCode |
[ "006:045" ] |
| publisher |
{ "name": "National Institute of Standards and Technology", "@type": "org:Organization" } |
| theme |
[ "Bioscience:Biomaterials", "Information Technology:Data and informatics", "Manufacturing:Biomanufacturing", "Nanotechnology:Nanobiotechnology" ] |
| title | A CTF-Based Data Augmentation Method for the Segmentation of Lipid Nanoparticles in Cryo-EM |
