EMPIAR-12660 - FIB-SEM Chinese Hamster Ovary cell line sample dataset [multiple data sets in TIFF and PNG formats]

EMPIAR-12660

FIB-SEM Chinese Hamster Ovary cell line sample dataset [multiple data sets in TIFF and PNG formats]

Publication:

Contextual High-throughput 3D Volume Electron Microscopy Data Acquisition Using Artificial Intelligence

Hurník Konečná T, Jančík R, Slamková D, Přibyl B, Tomova C, Rotkina L, Burch-Smith T, Sviben S, Fitzpatrick JAJ, Czymmek KJ

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Related EMDB entry:

Deposited:

2025-04-01

Released:

2025-06-30

Last modified:

2025-06-30

Imageset size:

1.28 GB

Imageset DOI:

10.6019/EMPIAR-12660

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
micrographs - single frame

Image Sets

1. FIB-SEM Chinese Hamster Ovary cell line sample dataset

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

1043

Image size:

(1536, 1324)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(90.0, 90.0)

Details:

Thermo Scientific Auto Slice & View (ASV), version 5 - Spin Mill

Files:

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

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

2. FIB-SEM Chinese Hamster Ovary cell line sample dataset - annotation by user on the first slice

Category:

micrographs - single frame

Image format:

PNG

No. of images or tilt series:

Image size:

(1534, 1324)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(90.0, 90.0)

Details:

Manual annotation by user on the first slice.

Files:

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

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

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

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Citations

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

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)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (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)