EMPIAR-10791 - High resolution 3D imaging of liver subcellular architecture and its link to metabolic function [multiple data sets in TIFF format]

EMPIAR-10791

High resolution 3D imaging of liver subcellular architecture and its link to metabolic function [multiple data sets in TIFF format]

Publication:

Regulation of liver subcellular architecture controls metabolic homeostasis

Parlakgul G, Arruda AP, Pang S, Cagampan E, Min N, Guney E, Lee Y, Inouye K, Hess HF, Xu CS, Hotamisligil GS

Nature (2022)

PMID: 35264794

DOI: 10.1038/s41586-022-04488-5

Related EMDB entry:

Deposited:

2021-08-13

Released:

2022-01-14

Last modified:

2022-03-11

Imageset size:

2.11 TB

Imageset DOI:

10.6019/EMPIAR-10791

Experimental metadata:

Download xml json

Contains:

reconstructed volumes

Image Sets

1. 6461 Lean Liver Dataset - FIB-SEM and Segmentation

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

5638

Image size:

(12000, 8000)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

6461 is Lean liver dataset - 12000 x 8000 x 5638 voxel, 8nm isotropic resolution.
There are 5638 consecutive raw FIBSEM images
and 5638 corresponding images in each segmentation class
(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane, Nuclear membrane)

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.

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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. 6464 Obese1 Liver Dataset - FIB-SEM and Segmentation

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

7896

Image size:

(9112, 10200)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

6464 is Obese1 liver dataset, 9112 x 10200 x 7896 voxel, 8nm isotropic resolution
There are 7896 consecutive raw FIBSEM images
and 7896 corresponding images in each segmentation class
(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane, Nuclear membrane)

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. 9430 Obese2 Liver Dataset - FIB-SEM and Segmentation

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

8501

Image size:

(8000, 8050)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

9430 is Obese2 liver dataset, 8000 x 8050 x 8501 voxel, 8nm isotropic resolution
There are 8501 consecutive raw FIBSEM images
and 8501 corresponding images in each segmentation class
(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane, Nuclear membrane)

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. 1857 Obese Climp63 Liver Dataset - FIB-SEM and Segmentation

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

3629

Image size:

(9700, 9650)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(8.0, 8.0)

Details:

1857 is Obese Climp63 liver dataset, 9700 x 9650 x 3629 voxel, 8nm isotropic resolution
There are 3629 consecutive raw FIBSEM images
and 3629 corresponding images in each segmentation class
(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane)

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. Segmentation Evaluation files - Manual annotation, prediction, raw data files

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(150, 150)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(16.0, 16.0)

Details:

The evaluation was performed on down-sampled data. A down-sampled version of the raw data is provided as well. Raw data, manual annotation data and predictions are provided as tiff stacks (8bit or 32bit, compressed, packaged in a .zip container). For lipid droplets, mitochondria, nuclear membrane and ER, we selected 3 test volumes of 300×300×50 voxels at random locations. Object based scores were only calculated for mitochondria and lipid droplets. For ER sheet and tubule evaluation, we randomly choose an area of 750x750 pixel^2 at 4 different locations in each dataset. Raw data, manual annotations and predictions are provided.

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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