EMPIAR-12464 - Heterogeneous Assembly of Herpesvirus Capsids In Situ Illuminated by Cryo-FIB/ET. [multiple data sets in MRC and TIFF formats]

EMPIAR-12464

Heterogeneous Assembly of Herpesvirus Capsids In Situ Illuminated by Cryo-FIB/ET. [multiple data sets in MRC and TIFF formats]

Publication:

Heterogeneous Assembly of Herpesvirus Capsids In Situ Illuminated by Cryo-FIB/ET.

Oliver SL

(---)

Related EMDB entry:

Deposited:

2024-11-11

Released:

2026-02-26

Last modified:

2026-02-26

Imageset size:

3.27 TB

Imageset DOI:

10.6019/EMPIAR-12464

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe
tilt series
reconstructed volumes

Image Sets

1. Gain Reference

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.376, 3.376)

Details:

Gain reference for session 20201229.

Files:

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2. Unaligned Tilt Series Frames.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

675

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.438, 3.438)

Details:

These are the individual frames for tilt series collected for session 20201229 by cryo-ET of lamella produced by cryo-FIB of VZV infected MeWo cells.

Files:

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3. Gain Reference

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.333, 3.333)

Details:

Gain reference for session 20211103.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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4. Unaligned Tilt Series Frames.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1619

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.44, 3.44)

Details:

These are the individual frames for tilt series collected for session 20211103 by cryo-ET of lamella produced by cryo-FIB of VZV infected MeWo cells.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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5. Gain Reference.

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.333, 3.333)

Details:

Gain reference for session 20211208.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

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6. Unaligned Tilt Series Frames.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

971

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.44, 3.44)

Details:

These are the individual frames for tilt series collected for session 20211208 by cryo-ET of lamella produced by cryo-FIB of VZV infected MeWo cells.

Files:

This entry cannot be downloaded from PDBj.

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7. Gain Reference.

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.333, 3.333)

Details:

Gain reference for session 20220507.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

8. Unaligned Tilt Series Frames.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1373

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.44, 3.44)

Details:

These are the individual frames for tilt series collected for session 20220507 by cryo-ET of lamella produced by cryo-FIB of VZV infected MeWo cells.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

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9. Gain Reference.

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.646, 2.646)

Details:

Gain reference for session 20220615.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

10. Unaligned Tilt Series Frames.

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

838

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.44, 3.44)

Details:

These are the individual frames for tilt series collected for session 20220615 by cryo-ET of lamella produced by cryo-FIB of VZV infected MeWo cells.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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11. EMAN2 Tilt Series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.44, 3.44)

Details:

Tilt series used to generate cryo-ET maps of the VZV capsid vertex and 3-fold axis of symmetry using EMAN2.

Files:

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12. Binned Tomograms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1022, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.76, 13.76)

Details:

These tomograms are binned by 4 and used to generate cryo-ET maps of the VZV portal vertex from B- and C-capsids. Frames per image 200 was used as a place holder as the thickness (Z) for each tomogram varies due to ice thickness of cryo-FIB lamella.

Files:

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13. IMOD Aligned Stacks for VZV Capsid Portal Processing

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

16 BIT FLOAT

Pixel spacing:

(3.44, 3.44)

Details:

This folder contains a subset of folders from IMOD alignments performed to generate files for input into the Relion 4 tomography pipeline.

Files:

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14. Segmentation using Dragonfly

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1023, 1440)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(13.76, 13.76)

Details:

This folder contains a reconstructed tomogram along with Dragonfly files used for training and segmentation. The individual segments are available in the ChimeraX-Segmentation folder.

Files:

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Citations

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)

Ultrathin liquid cells for microsecond time-resolved cryo-EM.

Curtis WA, Wenz J, Krüger CR, Barrass SV, Drabbels M, Lorenz UJ. (2026)

GTpick: A deep neural network for Cryo-EM particle detection.

Ni S, Yang C, Liu Y, Zhang Y, Shi Y, Qian A, Kong R, Chang S. (2025)

Species-specific structural adaptation of the potyviral coat protein in virions and virus-like particles.

Koritnik N, Kežar A, Kavčič L, Žnidarič MT, Leonardi A, De S, Pollari M, Mäkinen K, Podobnik M. (2026)

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

Arora S, Pan SH, Kumar S, Singh SK, Chauhan U, Alhalabi W, Arya V, Alsulami BS, Hsu CH, Chui KT, Gupta BB. (2025)

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