EMPIAR-10806 - electron cryo-tomograms of axons from human cerebral organoids, expressing membrane-targeted GFP [multiple data sets in MRC and MRCS formats]

EMPIAR-10806

electron cryo-tomograms of axons from human cerebral organoids, expressing membrane-targeted GFP [multiple data sets in MRC and MRCS formats]

Publication:

Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoids

Hoffmann P, Giandomenico S, Ganeva I, Wozny M, Sutcliffe M, Lancaster M, Kukulski W

eLife 10 (2021)

DOI: 10.7554/eLife.70269

Related EMDB entry:

EMD-13195

Deposited:

2021-07-13

Released:

2021-11-01

Last modified:

2021-11-01

Imageset size:

181.43 GB

Imageset DOI:

10.6019/EMPIAR-10806

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
micrographs - multiframe

Image Sets

1. reconstructed electron tomographic volumes of axons from human cerebral organoids expressing membrane-targeted GFP

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1920, 1854)

Pixel type:

SIGNED BYTE

Pixel spacing:

(None, None)

Details:

Tomograms were reconstructed with IMOD using back projection with a SIRT-like filter from stacks aligned by patch tracking, binning 2. Pixel sizes are 7.1 or 7.4 Å (check header).

Files:

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2. raw image frames of tilt series acquired on axons from human cerebral organoids expressing membrane-targeted GFP

Category:

micrographs - multiframe

Image format:

MRCS

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.5, 3.5)

Details:

22 folders, each corresponding to one tilt series and containing raw image frames as well as metadata in an .mdoc file. Image frames are not aligned. Image files contained in folders named starting with g4 are gain-corrected .mrcs files. Image files contained in folders named starting with g7 and g9 are not gain-corrected .tiff files. Two additional folders contain the respective gain reference and defect files. Tilt images in folders starting with g7 were acquired as 3 frames per image, all other tilt images were acquired as 4 frames per image. Pixel sizes are 3.5 Å for images in folders starting with g4, and 3.7 Å for all other images.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

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Citations

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Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

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Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (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)

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

He L, Bartesaghi A. (2026)

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Kong L, Zottig X, Elferich J, Grigorieff N. (2026)

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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)

Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (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)

See all citations

Protein Data Bank Japan News

[2026-06-10]

333件のPDBエントリーが新たに公開されました。（2026-06-10付）