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Institute of Neuroscience and Medicine – Structural and functional organisation of the brain (INM-1) (Forschungszentrum Jülich)
Replication Data for: From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging
Version 3.0
Oberstrass, Alexander; Vaca-Cerda, Esteban; Upschulte, Eric; Niu, Meiqi; Palomero-Gallagher, Nicola; Graessel, David; Schiffer, Christian; Axer, Markus; Amunts, Katrin; Dickscheid, Timo, 2025, "Replication Data for: From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging", https://doi.org/10.26165/JUELICH-DATA/ZOBFV7, Jülich DATA, V3
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Description
This dataset contains replication data for the article "From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging". It comprises 31 square regions of interest (ROIs, 4096 × 4096 px, 1.3 µm/px ≈ 5.3 mm), extracted from eight coronal sections of a healthy 2.4-year-old male vervet monkey brain at the level of the central sulcus. Section thickness is 60 µm. The dataset is divided into two subsets used for model training and testing in the article:
  • Training set ("train/"): 27 ROIs (0000–0026) with transmittance, retardation, direction, and affine-registered Cresyl violet.
  • Test set ("test/"): 4 ROIs (0027–0030) with transmittance, retardation, direction, fiber orientation maps, and non-linearly registered Cresyl violet. Also includes full 3D-PLI sections and model predictions (see article).
Each ROI is stored in HDF5 format with:
  • Dataset "Image": float32 for transmittance, retardation, and direction; uint8 for Cresyl violet.
  • Group "pyramid": down-sampled image levels.
  • Attribute "origin": location of the ROI within the corresponding full section in physical coordinates.
Full sections are available as BigTIFF images with 8 pyramid levels (uint8). Transmittance and retardation were normalized to the range 0-255 for visualization. Please refer to the research article for detailed information on sample preparation, imaging, data processing, registration, model training, and model inference. This dataset can be used under licence CC-BY-NC-SA (2025-03-21)
Subject Medicine, Health and Life Sciences
Notes The reference to the related publication "From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging" will be added as soon as released.
Institute INM-1
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0000_cresyl.h5
train/cresyl/
Hierarchical Data Format - 64.1 MB - Jun 18, 2025 - 1 Download
SHA-256: c4a8bff58471a4661256c9005ccc37b17e0df60b0e6d1bbbfbea52b94e42dc5b
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0000_direction.h5
train/direction/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: d61bf4b7d78621ce3f5007b27989d036cefe6f610494e1bebc65ee6f7655c5fa
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0000_retardation.h5
train/retardation/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: 9c2ef0780d7dc3a7551355584f980c702ff4532f8bac035a53a9e962270c43ac
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0000_transmittance.h5
train/transmittance/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: f2759c1735548e7c46ac3ff622386d8637c152a6f0e43b1d91daa50ececc8f54
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0001_cresyl.h5
train/cresyl/
Hierarchical Data Format - 64.1 MB - Jun 18, 2025 - 1 Download
SHA-256: 2b05aac7a9c9caa099821778348217589fbba994d6ad8d580f7d9c7f5537722f
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0001_direction.h5
train/direction/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: d5797ccbf67b9f82f25fa76165a9cda33aeb73ba6997aa3ee3b86eec3365f422
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0001_retardation.h5
train/retardation/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: b5aba278ec9366ceb1d8e3ea08ae032246b02fe41cf6a74c9d8c6dda000ca135
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0001_transmittance.h5
train/transmittance/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: 7d5aa72944fa17f2be05a03e14999256ae267f8b12e66f38484a5566ef6ad306
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0002_cresyl.h5
train/cresyl/
Hierarchical Data Format - 64.1 MB - Jun 18, 2025 - 1 Download
SHA-256: 650dfedb95c689fea6a70eb2cd1e1d35000326014c248eb7c8ce8e3a38c31b94
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0002_direction.h5
train/direction/
Hierarchical Data Format - 85.4 MB - Jun 18, 2025 - 1 Download
SHA-256: b8c8b6fc534c2ac79417735ee10a213ca72dc4cc456b9f149a5c806068b52326
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