EMPIAR-12176 - Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis [multiple data sets in TIFF and MRC formats]

EMPIAR-12176

Cryo-ET datasets (1 and 2) of dormant microporidian spores from Encephalitozoon intestinalis [multiple data sets in TIFF and MRC formats]

Publication:

Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites

Usmani M, Coudray N, Riggi M, Raghu R, Ramchandani H, Bobe D, Kopylov M, Zhong ED, Iwasa JH, Ekiert DC, Bhabha G

Proceedings of the National Academy of Sciences of the United States of America 122 (2025)

PMID: 40067903

DOI: 10.1073/pnas.2415233122

Related EMDB entry:

EMD-45674 EMD-45673

Deposited:

2024-06-11

Released:

2025-05-22

Last modified:

2025-05-22

Imageset size:

1.39 TB

Imageset DOI:

10.6019/EMPIAR-12176

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes

Image Sets

1. Raw frames from dataset 1 of microsporidian Encephalitozoon intestinalis

Category:

tilt series

Image format:

TIFF

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(2.076, 2.077)

Details:

Each tilt series is contained within its unique directory with an identifiable name. The folder called 'raw_frames' contains the raw frames and corresponding mdoc files from each tilt series.

Files:

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2. Unaligned tilt stacks from dataset 1 of microsporidian Encephalitozoon intestinalis

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.077, 2.077)

Details:

Each tilt series is contained within its unique directory with an identifiable name. The folder called 'tilt_series' contains the unaligned tilt stacks with corresponding tilt files. The aligned tilt series file can be found in 'aligned_tilt_series'.

Files:

This entry cannot be downloaded from PDBj.

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.

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3. Reconstructed tomograms from dataset 1 of microsporidian Encephalitozoon intestinalis

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

Each tomogram reconstruction is contained within its unique directory with an identifiable name. The folder called 'tomo_rec_4bin_SART' contains the 4 times binned volume reconstructed using aretomo as examples.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

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4. Raw frames from dataset 2 of microsporidian Encephalitozoon intestinalis

Category:

tilt series

Image format:

TIFF

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.676, 1.676)

Details:

Each tilt series is contained within its unique directory with an identifiable name. The folder called 'raw_frames' contains the raw frames and corresponding mdoc field from each tilt series. These data were collected with super resolution.

Files:

This entry cannot be downloaded from PDBj.

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)

5. Unaligned tilt stacks from dataset 2 of microsporidian Encephalitozoon intestinalis

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.353, 3.353)

Details:

Files:

This entry cannot be downloaded from PDBj.

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)

6. Reconstructed tomograms from dataset 2 of microsporidian Encephalitozoon intestinalis

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

Files:

This entry cannot be downloaded from PDBj.

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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Liu HF, Zhou Y, Huang Q, Martin J, Bartesaghi A. (2025)

CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles.

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Felix J, De Munck S, Bazan JF, Savvides SN. (2025)

Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE.

Van CTS, Reboul CF, Caesar JJE, Meana-Pañeda R, Lountos GT, Deme JC, Bryant OJ, Johnson S, Piczak CT, Valkov E, Lea SM, Elmlund H. (2025)

Cryo-EM Structure Reconstruction by Gaussian Splatting: Pushing the Resolution to Extreme

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