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Example data - Brain MRI dataset #135

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GenevieveBuckley opened this issue Apr 6, 2020 · 1 comment

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GenevieveBuckley commented Apr 6, 2020 •

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Example data - Brain MRI dataset

This great PR napari/napari.github.io#64 to the napari tutorials was made by partners @DaliaAymanAmeen and Dina for their RGSOC application. They use a beautiful MRI dataset of a human brain, and I think it would make a great example dataset for dask-image, too.

Link to main page: https://doi.org/10.5061/dryad.119f80q
License: This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.
Description: 7 Tesla MRI of the ex vivo human brain at 100 micron resolution. Includes axial, sagittal, and coronal imaging planes.

Direct download links (zip files containing a folder full of tiff images):

1.9GB zipped (expands to 4GB when unzipped). Synthesized_FLASH25_100um_TIF_Axial_Images.zip - https://datadryad.org/stash/downloads/file_stream/223913
1.9GB zipped (expands to 4GB when unzipped). Synthesized_FLASH25_100um_TIF_Coronal_Images.zip - https://datadryad.org/stash/downloads/file_stream/223914
1.9GB zipped (expands to 4GB when unzipped). Synthesized_FLASH25_100um_TIFF_Sagittal_Images.zip - https://datadryad.org/stash/downloads/file_stream/223915

PDF scan protocol file: https://datadryad.org/stash/downloads/file_stream/223924

MP4 movies of the data:

VIDEO_4_100_MICRON_MRI_SYNTHESIZED_FLASH25_AXIAL.mp4 - https://datadryad.org/stash/downloads/file_stream/223929
VIDEO_5_100_MICRON_MRI_SYNTHESIZED_FLASH25_CORONAL.mp4 - https://datadryad.org/stash/downloads/file_stream/223930
VIDEO_6_100_MICRON_MRI_SYNTHESIZED_FLASH25_SAGITTAL.mp4 - https://datadryad.org/stash/downloads/file_stream/223931

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GenevieveBuckley commented Apr 6, 2020

Apparently there's an OpenNeuro mirror, but downloads here seem flaky & slower (I've had one download attempt fail already).

OpenNeuro mirror: https://openneuro.org/datasets/ds002179

Direct download links:

Synthesized_FLASH25_100um_TIFF_Axial_Images.zip - https://openneuro.org/crn/datasets/ds002179/snapshots/1.1.0/files/derivatives:sub-EXC004:synthesized_FLASH25_100um_tiff_images:Synthesized_FLASH25_100um_TIFF_Axial_Images.zip
Synthesized_FLASH25_100um_TIFF_Coronal_Images.zip - https://openneuro.org/crn/datasets/ds002179/snapshots/1.1.0/files/derivatives:sub-EXC004:synthesized_FLASH25_100um_tiff_images:Synthesized_FLASH25_100um_TIFF_Coronal_Images.zip
Synthesized_FLASH25_100um_TIFF_Sagittal_Images.zip - https://openneuro.org/crn/datasets/ds002179/snapshots/1.1.0/files/derivatives:sub-EXC004:synthesized_FLASH25_100um_tiff_images:Synthesized_FLASH25_100um_TIFF_Sagittal_Images.zip

Youtube playlist: https://www.youtube.com/playlist?list=PLlL7CEMX5bxzl1TqkJRK3pMV4Ax6By4bN

Paper link: https://www.nature.com/articles/s41597-019-0254-8

GenevieveBuckley mentioned this issue

Demo dataset infrastructure #246

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GenevieveBuckley mentioned this issue

Image analysis coiled/benchmarks#751

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