EMPIAR-10490 - Integrative imaging reveals SARS-CoV-2 induced reshaping of subcellular morphology [multiple data sets in MRC, BIG DATA VIEWER HDF5 and TIFF formats]

EMPIAR-10490

Integrative imaging reveals SARS-CoV-2 induced reshaping of subcellular morphology [multiple data sets in MRC, BIG DATA VIEWER HDF5 and TIFF formats]

Publication:

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies

Cortese M, Lee JY, Cerikan B, Neufeldt CJ, Oorschot VMJ, Köhrer S, Hennies J, Schieber NL, Ronchi P, Mizzon G, Romero-Brey I, Santarella-Mellwig R, Schorb M, Boermel M, Mocaer K, Beckwith MS, Templin RM, Gross V, Pape C, Tischer C, Frankish J, Horvat NK, Laketa V, Stanifer M, Boulant S, Ruggieri A, Chatel-Chaix L, Schwab Y, Bartenschlager R

Cell host & microbe (2020)

PMID: 33245857

DOI: 10.1016/j.chom.2020.11.003

Related EMDB entry:

EMD-12940

Deposited:

2020-06-24

Released:

2020-12-11

Last modified:

2021-10-25

Imageset size:

1.15 TB

Imageset DOI:

10.6019/EMPIAR-10490

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes
micrographs - single frame

Image Sets

1. MOI0.5-24h-Dual axis tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

202

Image size:

(2024, 2024)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 0.5, 24h post infection;
Dual axis tilt series, both axes as individual *.st MRC files

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.

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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

2. MOI5-12h-Dual axis tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

178

Image size:

(2024, 2024)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 5, 12h post infection;
Dual axis tilt series, both axes as individual *.st MRC files

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. MOI5-24h-Dual axis tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

152

Image size:

(2024, 2024)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 5, 24h post infection;
Dual axis tilt series, both axes as individual *.st MRC files

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. MOI5-6h-Dual axis tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(2024, 2024)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 5, 6h post infection;
Dual axis tilt series, both axes as individual *.st MRC files

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)

5. MOI0.5-24h-Reconstructed tomograms

Category:

reconstructed volumes

Image format:

BIG DATA VIEWER HDF5

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 0.5, 24h post infection;
Reconstructed volume from dual axis tilt series, BDV HDF5 format, positioned according to physical location on specimen. Corresponding map files for targeting in adjacent "maps" directory.

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)

6. MOI5-12h-Reconstructed tomograms

Category:

reconstructed volumes

Image format:

BIG DATA VIEWER HDF5

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 5, 12h post infection;
Reconstructed volume from dual axis tilt series, BDV HDF5 format, positioned according to physical location on specimen. Corresponding map files for targeting in adjacent "maps" directory.

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)

7. MOI5-24h-Reconstructed tomograms

Category:

reconstructed volumes

Image format:

BIG DATA VIEWER HDF5

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 5, 24h post infection;
Reconstructed volume from dual axis tilt series, BDV HDF5 format, positioned according to physical location on specimen. Corresponding map files for targeting in adjacent "maps" directory.

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)

8. MOI5-6h-Reconstructed tomograms

Category:

reconstructed volumes

Image format:

BIG DATA VIEWER HDF5

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(15.578, 15.578)

Details:

Condition: MOI = 5, 6h post infection;
Reconstructed volume from dual axis tilt series, BDV HDF5 format, positioned according to physical location on specimen. Corresponding map files for targeting in adjacent "maps" directory.

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)

9. S4 Area 2 FIB-SEM Volume 8nm isotropic

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

4824

Image size:

(3864, 3144)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(80.0, 80.0)

Details:

S4 Area 2 FIB-SEM Volume 8nm isotropic voxel size, aligned

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)

10. S4 Area 3 FIB-SEM Volume 8nm isotropic

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

4413

Image size:

(5632, 3648)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(80.0, 80.0)

Details:

S4 Area 3 FIB-SEM Volume 8nm isotropic voxel size, aligned

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)

11. S4 Cell 1 FIB-SEM Volume 5nm isotropic

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

11199

Image size:

(7512, 3864)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(50.0, 50.0)

Details:

S4 Cell 1 FIB-SEM Volume 5nm isotropic voxel size, aligned

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)

12. S5 Mock Cell 1 FIB-SEM Volume 8nm isotropic

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

2574

Image size:

(6624, 4236)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(80.0, 80.0)

Details:

S5 Mock/Control Cell 1 FIB-SEM Volume 8nm isotropic voxel size, aligned

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)

13. Mock cells - Dual axis tilt series

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(2024, 2024)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(15.578, 15.578)

Details:

Condition: Mock;
Dual axis tilt series, both axes as individual *.st MRC files

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)

14. Mock cells-Reconstructed tomograms

Category:

reconstructed volumes

Image format:

BIG DATA VIEWER HDF5

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(15.578, 15.578)

Details:

Condition: Mock;
Reconstructed volume from dual axis tilt series, BDV HDF5 format, positioned according to physical location on specimen. Corresponding map files for targeting in adjacent "maps" directory.

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

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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