EMPIAR-13281 - cryo electron tomography of mouse hippocampal CA1 stratum radiatum - dataset 2 [multiple data sets in EER and MRC formats]

EMPIAR-13281

cryo electron tomography of mouse hippocampal CA1 stratum radiatum - dataset 2 [multiple data sets in EER and MRC formats]

Publication:

A generalizable and targeted molecular biopsy approach for in situ cryogenic electron tomography of vitreous brain tissue

Glynn C, Smith JLR, Case M, Csöndör R, Katsini A, Sanita ME, Glen TS, Pennington A, Grange M

Cell reports methods 5 (2025)

PMID: 40527314

DOI: 10.1016/j.crmeth.2025.101080

Related EMDB entry:

EMD-55442

Deposited:

2025-10-20

Released:

2026-03-13

Last modified:

2026-03-13

Imageset size:

740.95 GB

Imageset DOI:

10.6019/EMPIAR-13281

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes

Image Sets

1. raw eer of tilt series

Category:

tilt series

Image format:

EER

No. of images or tilt series:

145

Image size:

(4096, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.98, 1.98)

Details:

130 e/A^2 total dose. 3.17e/A2/tilt. Tilts collected dose symmetrically with 3 degrees between tilts.

Files:

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2. raw .mrc of tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

145

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.98, 1.98)

Details:

130e-/A^2 total doze. 3.17e-/A2/tilt. Tilts collected dose symmetrically with 3 degrees between tilts.

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.

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)

3. unfiltered bin 8 reconstructions

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

145

Image size:

(512, 512)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(15.84, 15.84)

Details:

unfiltered bin 8 reconstructions using aretomo2.

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.

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

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)

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

He L, Bartesaghi A. (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)