EMPIAR-12535 - Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos [multiple data sets in TIFF format]

EMPIAR-12535

Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos [multiple data sets in TIFF format]

Publication:

Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos

Jiang Y, Wang H, Boergens K, Rzepka N, Wang F, Hua Y

Cell Reports Methods 5 (2025)

DOI: 10.1016/j.crmeth.2025.100989

Related EMDB entry:

Deposited:

2025-01-24

Released:

2025-03-20

Last modified:

2025-03-20

Imageset size:

996.43 GB

Imageset DOI:

10.6019/EMPIAR-12535

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. HuaLab-mouse-intestinal-tissue-raw

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1000

Image size:

(6808, 5024)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

HuaLab-mouse-intestinal-tissue-raw contains 1000 three-dimensional continuous images collected by Serial Section SEM, which have been aligned, contrast adjusted, and converted into 8-bit images with voxel resolution of 8nm * 8nm * 50nm.

Files:

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2. HuaLab-mouse-mouse-testis-tissue-raw

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2605

Image size:

(10419, 4884)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

HuaLab-mouse-mouse-testis-tissue-raw contains 2605 three-dimensional continuous images collected by SBF-SEM, which have been aligned, contrast adjusted, and converted into 8-bit images with voxel resolution of 15nm * 15nm * 50nm.

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. Hualab-DCN-A23-CBA-2M-raw

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3893

Image size:

(15303, 16449)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

Hualab-DCN-A23-CBA-2M-raw contains 3893 three-dimensional continuous images collected by SBF-SEM, which have been aligned, contrast adjusted, and converted into 8-bit images with voxel resolution of 15nm * 15nm * 50nm.

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

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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)