EMPIAR-12661 - FIB-SEM Trypanosoma cruzi cell samples [multiple data sets in TIFF and PNG formats]

EMPIAR-12661

FIB-SEM Trypanosoma cruzi cell samples [multiple data sets in TIFF and PNG formats]

Publication:

Contextual High-throughput 3D Volume Electron Microscopy Data Acquisition Using Artificial Intelligence

Hurník Konečná T, Jančík R, Slamková D, Přibyl B, Tomova C, Rotkina L, Burch-Smith T, Sviben S, Fitzpatrick JAJ, Czymmek KJ

(---)

Related EMDB entry:

Deposited:

2025-04-01

Released:

2025-06-30

Last modified:

2025-06-30

Imageset size:

10.81 GB

Imageset DOI:

10.6019/EMPIAR-12661

Experimental metadata:

Download xml json

Contains:

reconstructed volumes

Image Sets

1. FIB-SEM Trypanosoma cruzi cell samples - merge images

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

488

Image size:

(3807, 2402)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Combination of rescale low-resolution background and high-resolution ROI.

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. FIB-SEM Trypanosoma cruzi cell samples - low-resolution

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

488

Image size:

(1523, 961)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(250.0, 250.0)

Details:

---

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. FIB-SEM Trypanosoma cruzi cell samples - high-resolution

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

488

Image size:

(3807, 2402)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

---

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. FIB-SEM Trypanosoma cruzi cell samples - annotation of the first slice

Category:

reconstructed volumes

Image format:

PNG

No. of images or tilt series:

Image size:

(3807, 2402)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Manual annotation of the fist slice.

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)