Open Data

3Scan offers these tissue data subsets openly and free of use to all. Please contact us if you would like to receive a USB drive with the full samples.


Mouse kidney microvasculature – 1 gigavoxel

3D render of kidney vasculature subset

A mouse kidney was perfused with India Ink, staining all vasculature. This dataset is 1 gigavoxel (GV, 1 billion voxels or 3D pixels), comprising 1.1% of the total kidney sample volume (89.4 GV). This 3D volume represents 0.003 cm3 from a total volume of 0.25 cm3.


Download dataset here [480 MB zip]
kidney vasculature subset 3D render [36 MB mp4]
2D Z flythrough video [13.3 MB mp4]


Region shape: 2048 x 2048  x 250
Total number of voxels: 1.049 GV
Size in memory (uncompressed): 1.049 GB
Voxel size (um):  0.7, 0.7, 6


1 GV mouse kidney vasculature 3D render

Maximum intensity projection 3D render of india ink stained kidney

2D india ink face, 2048x2048

2D face india ink stain, 2048×2048 pixels. Click for full resolution



Mouse intestine – 5 gigavoxel

A mouse intestine was whole-mount stained with H&E. Cell nuclei and other acidic structures are stained blue with hematoxylin, alkaline structures are stained pink with eosin. This dataset is 5.25 GV, comprising 4.1% of the total intestine sample (147.3 GV). This 3D volume represents 0.033 cm3 from a total volume of 1.0 cm3.


Download dataset here [9.1 GB zip] Note that FAT32 filesystems will not be able to store this file because of the maximum file size limit.
2D Z flythrough video [88 MB mp4]


Region shape: 6000 x 3500 x 250 x 3)
Total number of voxels: 5.250 GV
Size in memory (uncompressed): 15.750 GB
Voxel size (um): 1.056, 1.056, 6


H&E mouse intestine face, downsampled 25%

2D H&E mouse intestine face, downsampled 25%. Click image to download full resolution (38 MB)

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