EMPIAR-11958 - Volume correlative light X-ray and electron microscopy (CLXEM) of mouse cremaster muscle endothelial cells [multiple data sets in TIFF format]

EMPIAR-11958

Volume correlative light X-ray and electron microscopy (CLXEM) of mouse cremaster muscle endothelial cells [multiple data sets in TIFF format]

Publication:

Volume correlative light X-ray and electron microscopy (CLXEM) of endothelial cells in mouse tissue

Reglero-Real N, Pérez-Gutiérrez L, Saleeb RS, Nourshargh S, Collinson L, Yoshimura A

STAR Protocols (---)

DOI: 10.1016/j.xpro.2024.103257

Related EMDB entry:

Deposited:

2024-02-18

Released:

2024-09-03

Last modified:

2024-09-03

Imageset size:

79.21 GB

Imageset DOI:

10.6019/EMPIAR-11958

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
micrographs - multiframe

Image Sets

1. X-ray micro-computed tomography (µCT) of resin-embedded mouse cremaster muscle tissue

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(1004, 1024)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(74181.0, 74181.0)

Details:

Mouse cremaster muscle tissue containing the region of interest previously imaged by confocal laser scanning microscopy. Light microscopy data is available in BioStudies.

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. X-ray µCT of resin-embedded mouse cremaster muscle tissue after first trimming around the region of interest

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(992, 1015)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(32635.0, 32635.0)

Details:

Mouse cremaster muscle tissue containing the region of interest previously imaged by confocal laser scanning microscopy. Light microscopy data is available in BioStudies.

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. X-ray µCT of resin-embedded mouse cremaster muscle tissue after final trimming before SBF-SEM

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(992, 1015)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(10313.0, 10313.0)

Details:

Mouse cremaster muscle tissue containing the region of interest previously imaged by confocal laser scanning microscopy. Light microscopy data is available in BioStudies.

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)

4. SBF-SEM of the target endothelial cells identified by correlation of X-ray and light microscopy

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(9348, 13946)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(84.4, 500.0)

Details:

Data set of two SBF SEM acquisitions combined, aligned and processed as a tiff stack at the original resolution of acquisition.

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)

Browse All Files

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

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)