Segmentation of lipid nanoparticles from cryogenic electron microscopy images
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. Four sample types were prepared: LNPs in the presence and absence of RNA, and with LNPs ejected into pH 4 and pH 7.4 buffer after microfluidic assembly. To prepare samples for imaging, 3 ?L 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 ?m, 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. A total of 38 images were manually segmented into particle and non-particle regions. Segmentation masks and their corresponding images are deposited in this data set.
Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| accrualPeriodicity | irregular |
| 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. Four sample types were prepared: LNPs in the presence and absence of RNA, and with LNPs ejected into pH 4 and pH 7.4 buffer after microfluidic assembly. To prepare samples for imaging, 3 ?L 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 ?m, 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. A total of 38 images were manually segmented into particle and non-particle regions. Segmentation masks and their corresponding images are deposited in this data set. |
| distribution |
[
{
"title": "KC2 LNPs at pH 4, without RNA",
"format": ".zip archive containing TIFF images",
"mediaType": "application/x-zip-compressed",
"description": "CryoEM images of lipid nanoparticles and their segmentation masks",
"downloadURL": "https://data.nist.gov/od/ds/mds2-2753/R111_S404_pH4_1p5pcPEG_noRNA.zip"
},
{
"title": "KC2 LNPs at pH 7, without RNA",
"format": ".zip archive containing TIFF images",
"mediaType": "application/x-zip-compressed",
"description": "CryoEM images of lipid nanoparticles and their segmentation masks",
"downloadURL": "https://data.nist.gov/od/ds/mds2-2753/R111_S405_pH7_1p5pcPEG_noRNA.zip"
},
{
"title": "KC2 LNPs at pH 4, with RNA",
"format": ".zip archive containing TIFF images",
"mediaType": "application/x-zip-compressed",
"description": "CryoEM images of lipid nanoparticles and their segmentation masks",
"downloadURL": "https://data.nist.gov/od/ds/mds2-2753/R111_S406_pH4_1p5pcPEG_RNA.zip"
},
{
"title": "KC2 LNPs at pH 7, with RNA",
"format": ".zip archive containing TIFF images",
"mediaType": "application/x-zip-compressed",
"description": "CryoEM images of lipid nanoparticles and their segmentation masks",
"downloadURL": "https://data.nist.gov/od/ds/mds2-2753/R111_S407_pH7_1p5pcPEG_RNA.zip"
},
{
"title": "Readme",
"mediaType": "text/plain",
"downloadURL": "https://data.nist.gov/od/ds/mds2-2753/readme.txt"
}
]
|
| identifier | ark:/88434/mds2-2753 |
| issued | 2023-02-01 |
| keyword |
[
"AI",
"CryoEM",
"LNP",
"Lipid Nanoparticle",
"cryogenic electron microscopy",
"mRNA",
"machine learning"
]
|
| landingPage | https://data.nist.gov/od/id/mds2-2753 |
| language |
[
"en"
]
|
| license | https://www.nist.gov/open/license |
| modified | 2022-08-18 00:00:00 |
| programCode |
[
"006:045"
]
|
| publisher |
{
"name": "National Institute of Standards and Technology",
"@type": "org:Organization"
}
|
| references |
[
"https://doi.org/10.1038/s42003-021-02441-2"
]
|
| theme |
[
"Bioscience:Biomaterials",
"Information Technology:Computational science",
"Information Technology:Software research",
"Nanotechnology:Nanobiotechnology",
"Physics:Biological physics"
]
|
| title | Segmentation of lipid nanoparticles from cryogenic electron microscopy images |
