EMPIAR-12017 - Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity [multiple data sets in TIFF format]

EMPIAR-12017

Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity [multiple data sets in TIFF format]

Publication:

Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity

Parlakgul G, Pang S, Artico LL E, Min N, Cagampan E, Villa R, Goncalves RLS, Lee Y, Xu SC, Hotamisligil GS, Arruda AP

Nature Communications (2024)

Related EMDB entry:

Deposited:

2024-04-04

Released:

2024-04-17

Last modified:

2024-04-17

Imageset size:

2.89 TB

Imageset DOI:

10.6019/EMPIAR-12017

Experimental metadata:

Download xml json

Contains:

reconstructed volumes
micrographs - multiframe

Image Sets

1. 9428 Lean Fasted Liver Dataset - FIB-SEM and Segmentations

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

9501

Image size:

(7984, 6984)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.
Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
9498 is Lean Fasted Liver (7984 x 6984 x 9501 pixels in x, y, z)
There are 9501 consecutive raw FIBSEM images and 9501 corresponding images in each segmentation class.
Raw (8-bit): 493 Gb
ER (8-bit): 493 Gb (uncompressed size)
Mitochondria instance (32-bit): 1.9 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier
Lipid Droplet (8-bit): 493 Gb (uncompressed size)
Cell Membrane (8-bit): 493 Gb (uncompressed size) - each individual cell has a unique pixel intensity as an identifier
Nuclear membrane (8-bit): 493 Gb (uncompressed size)

Files:

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

2. 8970 Obese Fasted Liver Dataset - FIB-SEM and Segmentations

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

8450

Image size:

(9402, 6949)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.
Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
8970 is Obese Fasted Liver (9402 x 6949 x 8450 pixels in x, y, z)
There are 8450 consecutive raw FIBSEM images and 8450 corresponding images in each segmentation class.
Raw (8-bit): 514 Gb
ER (8-bit): 514 Gb (uncompressed size)
Mitochondria instance (32-bit): 2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier
Lipid Droplet (8-bit): 514 Gb (uncompressed size)
Cell Membrane (8-bit): 514 Gb (uncompressed size) - each individual cell has a unique pixel intensity as an identifier
Nuclear membrane (8-bit): 514 Gb (uncompressed size)

Files:

This entry cannot be downloaded from PDBj.

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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)

3. 6461 Lean Fed Liver Dataset - Mitochondria instance segmentations

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

5638

Image size:

(12000, 8000)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(8.0, 8.0)

Details:

Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes. Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
6461 is Lean Fed Liver (12000 x 8000 x 5638 pixels in x, y, z)
Mitochondria instance (32-bit): 2.16 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.
Raw and other segmentation classes can be found at https://www.ebi.ac.uk/empiar/EMPIAR-10791/

Files:

This entry cannot be downloaded from PDBj.

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

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4. 6464 Obese Fed Liver Dataset - Mitochondria instance segmentations

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

7896

Image size:

(9112, 10200)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(8.0, 8.0)

Details:

Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes. Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
6464 is Obese Fed Liver (9112 x 10200 x 7896 pixels in x, y, z)
Mitochondria instance (32-bit): 3 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.
Raw and other segmentation classes can be found at https://www.ebi.ac.uk/empiar/EMPIAR-10791/

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

5. 1931 - Pericentral Liver Dataset - FIB-SEM images

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

10777

Image size:

(8125, 8125)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

Raw FIBSEM images are not compressed and can be viewed online.
Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
1931 - Pericentral (lean fed liver) (8125 x 8125 x 10777 pixels in x, y, z)
There are 10777 consecutive raw FIBSEM images.

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. 1931 - Periportal Liver Dataset - FIB-SEM images

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

8982

Image size:

(6500, 6500)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

Raw FIBSEM images are not compressed and can be viewed online.
Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
1931 - Periportal (lean fed liver) (6500 x 6500 x 8982 pixels in x, y, z)
There are 8982 consecutive raw FIBSEM images.

Files:

This entry cannot be downloaded from PDBj.

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

7. 2679 Obese LacZ Liver Dataset - FIB-SEM and Segmentations

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

7705

Image size:

(6500, 6500)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.
Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
2679 is Obese liver expressing LacZ control (6500 x 6500 x 7705 pixels in x, y, z)
There are 7705 consecutive raw FIBSEM images and 3629 corresponding images in each segmentation class.
Raw (8-bit): 303 Gb
ER (8-bit): 303 Gb (uncompressed size)
Mitochondria instance (32-bit): 1.2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier

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)

8. 1858 Obese RRBP1 (p180) Liver Dataset - FIB-SEM and Segmentations

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

5860

Image size:

(9375, 10625)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.
Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).
1858 is Obese liver expressing RRBP1 (9375 x 10625 x 5860 pixels in x, y, z)
Please delete the first 65 images in each class (raw + segmentation). Firs 65 images contain the Durcupan resin.
There are 5860 consecutive raw FIBSEM images and 5860 corresponding images in each segmentation class.
Raw (8-bit): 544 Gb
ER (8-bit): 544 Gb (uncompressed size)
Mitochondria instance (32-bit): 2.2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.

Files:

This entry cannot be downloaded from PDBj.

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