Replication Data for: From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging

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	0000_cresyl.h5 cresyl/ Hierarchical Data Format - 64.1 MB - Mar 24, 2025 - 0 Downloads SHA-256: c4a8bff58471a4661256c9005ccc37b17e0df60b0e6d1bbbfbea52b94e42dc5b	Download
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	0002_cresyl.h5 cresyl/ Hierarchical Data Format - 64.1 MB - Mar 24, 2025 - 0 Downloads SHA-256: 650dfedb95c689fea6a70eb2cd1e1d35000326014c248eb7c8ce8e3a38c31b94	Download
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Citation Metadata

Dataset Persistent ID	doi:10.26165/JUELICH-DATA/ZOBFV7
Publication Date	2025-03-24
Title	Replication Data for: From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging
Author	Oberstrass, Alexander (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Helmholtz AI, Research Centre Jülich, Germany) - ORCID: 0000-0003-0712-034X Vaca-Cerda, Esteban (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Helmholtz AI, Research Centre Jülich, Germany) - ORCID: 0000-0003-0217-7208 Upschulte, Eric (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Helmholtz AI, Research Centre Jülich, Germany & Cécile & Oskar Vogt Institute of Brain Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany) - ORCID: 0000-0002-6398-038X Niu, Meiqi (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany) - ORCID: 0000-0001-7937-5814 Palomero-Gallagher, Nicola (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany) - ORCID: 0000-0003-4463-8578 Graessel, David (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany) - ORCID: 0000-0003-3228-8048 Schiffer, Christian (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Helmholtz AI, Research Centre Jülich, Germany) - ORCID: 0000-0002-2544-843X Axer, Markus (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Department of Physics, University of Wuppertal, Germany) - ORCID: 0000-0001-5871-9331 Amunts, Katrin (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Cécile & Oskar Vogt Institute of Brain Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany) - ORCID: 0000-0001-5828-0867 Dickscheid, Timo (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Helmholtz AI, Research Centre Jülich, Germany & Institute of Computer Science, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany) - ORCID: 0000-0002-9051-3701
Contact	Use email button above to contact. Oberstrass, Alexander (Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany & Helmholtz AI, Research Centre Jülich, Germany)
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), each measuring 4,069 pixels (~5.3 mm), extracted from eight coronal sections of a vervet monkey brain at the level of the central sulcus. All sections were imaged using 3D-Polarized Light Imaging (3D-PLI) to visualize nerve fibers and subsequently post-stained with Cresyl violet to highlight cell bodies. The ROIs are stored in HDF5 format, with image data stored under the "Image" dataset. The dataset is divided into two subsets used for model training and testing in the article: Training set ("train/"): Contains 27 ROIs, labeled 0000 to 0026, with 3D-PLI modalities (transmittance, direction, and retardation) alongside affine-registered Cresyl violet post-staining. Test set ("test/"): Contains 4 ROIs, labeled 0027 to 0030, with 3D-PLI modalities (transmittance, direction, retardation, and fiber orientation maps) alongside nonlinear registered Cresyl violet post-staining. Model predictions from GAN, Gram, GAN+Reg, and Gram+Reg models are provided for the test data under "test/predictions". Please refer to the research article for more information on the sample preparation, measurements, data processing, model specifications, training and inference procedures. 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.
Depositor	Wenzel, Susanne
Deposit Date	2025-03-21

FZJ Metadata

Institute	INM-1
PoF IV topic	Brain Function (POF4-351)

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