Multimodal 3-D histology atlas volumes and plates for developing human brains
Data files
Jan 09, 2025 version files 11.64 GB
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FB10_GW21_CCF.zip
4.06 GB
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FB3_GW21.zip
3.91 GB
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FB36_GW13.zip
950.57 MB
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FB40_GW13_CCF.zip
1.58 GB
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FB63_GW13.zip
1.13 GB
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README.md
1.65 KB
Abstract
This is a dataset accompanying a manuscript on a multimodal set of reference brains in a standardized coordinate framework for the developing human brain. Datasets for 5 brains are shared here corresponding to a range of gestational weeks from 13 to 21. Included are MRI, Nissl, and H&E volumes in a standardized coordinate system as well as a set of atlas plates.
README: Multimodal 3-D histology atlas volumes and plates for developing human brains
https://doi.org/10.5061/dryad.crjdfn3f3
Description of the data and file structure
The data was collected through histological procedures on whole brain specimens which were digitized at 0.5 um per pixel in-plane resolution and were used to create the dataset volumes
Files and variables
The following folder structure and data files are given:
- FB10_GW21_CCF.zip
- FB40_GW13_CCF.zip
- FB63_GW13.zip
- FB36_GW13.zip
- FB3_GW21.zip
- Each of the zipped files contains the following Folder structure
- average*age*space (FB3 as an example)
- FB3_HEReg_to_timeaverage.vtk.zip
- FB3_MRIReg_to_timeaverage.vtk.zip
- FB3_NisslReg_to_timeaverage.vtk.zip
- ras*_*space (FB3 as an example)
- FB3_HEReg_to_FB10_RAS.vtk.zip
- FB3_MRIReg_to_FB10_RAS.vtk.zip
- FB3_NisslReg_to_FB10_RAS.vtk.zip
- registerd*_*space (FB3 as an example)
- FB3_HEReg.vtk.zip
- FB3_MRIReg_uint8.vtk.zip
- FB3_NisslReg.vtk.zip
- Along with the segmentations file for the CCF brains (FB10 and FB40)
- FB10_SegsReg.vtk
Code/software
ITK-SNAP, Slicer 3D
This data can be loaded in Python or Matlab using loaders provided in
https://github.com/twardlab/emlddmm
or by reading the file specifications by implementing readers following the file specification for simple legacy vtk format here https://docs.vtk.org/en/latest/design_documents/VTKFileFormats.html