EMPIAR-13009 - Cryo electron tomography of wild-type Drosophila nephrocytes [multiple data sets in MRC format]

EMPIAR-13009

Cryo electron tomography of wild-type Drosophila nephrocytes [multiple data sets in MRC format]

Publication:

The slit diaphragm in Drosophila exhibits a bilayered, fishnet architecture

Moser D, Lang K, Birtasu AN, Grahammer F, Helmstaedter M, Scheffer MP, Hermle T, Frangakis AF

(---)

DOI: 10.1038/s41467-025-64347-5

Related EMDB entry:

EMD-53557

Deposited:

2025-08-27

Released:

2025-12-07

Last modified:

2025-12-07

Imageset size:

1.48 TB

Imageset DOI:

10.6019/EMPIAR-13009

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
tilt series
reconstructed volumes

Image Sets

1. Unaligned multi-frame micrographs of wild-type nephrocytes displaying slit diaphragms

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

SIGNED BYTE

Pixel spacing:

(1.339, 1.339)

Details:

Unaligned multi-frame micrographs acquired in super-resolution mode (pixel size 1.34A), with 41-58 micrographs per tilt-series. The corresponding .mdoc files containing the metadata for each tilt-series are in the subdirecory "mdoc", following the naming tomoXX.mrc.mdoc, with XX corresponding to the tilt-series ID.

Files:

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2. Unaligned tilt-series and alignment metadata

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.679, 2.679)

Details:

Unaligned tilt-series (tomoXX.st) and IMOD's etomo alignment metadata for each tilt-series (tomoXX.xf, tomoXX.tlt). XX corresponds to the tilt-series ID.

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)

3. Reconstructed tomograms of wild-type nephrocytes displaying slit diaphragms

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(1024, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(10.72, 10.72)

Details:

Reconstructed volumes of wild-type nephrocytes displaying slit diaphragms (rec_tomoXX.mrc, XX corresponds to tilt-series IDs).

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

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)