REL 2024-04-04 2024-04-17 2024-05-20 Gunes Parlakgul University of California, Berkeley 119 Morgan Hall Berkeley CA United States 94720 Gokhan S Hotamisligil Harvard TH Chan School of Public Health 665 Huntington Ave SPH1 Rm610 Boston MA United States 02115 Ana Paula Arruda University of California, Berkeley 129 Morgan Hall Berkeley CA United States 94720 Parlakgul G 2.9 10.6019/EMPIAR-12017 FIB-SEM tissue Parlakgül G Pang S Artico LL Min N Cagampan E Villa R Goncalves RLS Lee GY Xu CS Hotamışlıgil GS Arruda AP Nature communications Nat Commun United States 1 15 2024 English 10.1038/s41467-024-48272-7 38729945

Raw FIB-SEM imaging datasets and segmented classes from mouse liver tissues. 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) 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) 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/ 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/ 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 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 1931 - Pericentral (lean fed liver) (8125 x 8125 x 10777 pixels in x, y, z) There are 10777 consecutive raw FIBSEM images. 1931 - Periportal (lean fed liver) (6500 x 6500 x 8982 pixels in x, y, z) There are 8982 consecutive raw FIBSEM images.

EMPIAR-10791 9428 Lean Fasted Liver Dataset - FIB-SEM and Segmentations /data/9428 Lean Fasted reconstructed volumes TIFF TIFF 9501 1 UNSIGNED BYTE 7984 8.0 6984 8.0

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)

8970 Obese Fasted Liver Dataset - FIB-SEM and Segmentations /data/8970 Obese Fasted reconstructed volumes TIFF TIFF 8450 1 UNSIGNED BYTE 9402 8.0 6949 8.0

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)

6461 Lean Fed Liver Dataset - Mitochondria instance segmentations /data/Lean Fed reconstructed volumes TIFF TIFF 5638 1 32 BIT FLOAT 12000 8.0 8000 8.0

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/

6464 Obese Fed Liver Dataset - Mitochondria instance segmentations /data/Obese Fed reconstructed volumes TIFF TIFF 7896 1 32 BIT FLOAT 9112 8.0 10200 8.0

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/

1931 - Pericentral Liver Dataset - FIB-SEM images /data/Pericentral micrographs - multiframe TIFF TIFF 10777 1 UNSIGNED BYTE 8125 8.0 8125 8.0

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.

1931 - Periportal Liver Dataset - FIB-SEM images /data/Periportal micrographs - multiframe TIFF TIFF 8982 1 UNSIGNED BYTE 6500 8.0 6500 8.0

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.

2679 Obese LacZ Liver Dataset - FIB-SEM and Segmentations /data/Obese LacZ reconstructed volumes TIFF TIFF 7705 1 UNSIGNED BYTE 6500 8.0 6500 8.0

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

1858 Obese RRBP1 (p180) Liver Dataset - FIB-SEM and Segmentations /data/Obese RRBP1 reconstructed volumes TIFF TIFF 5860 1 UNSIGNED BYTE 9375 8.0 10625 8.0

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.