Mean diffusivity (MD) and fractional anisotropy (FA) obtained with diffusion tensor imaging (DTI) have been associated with cell density and tissue anisotropy across tumors, but these associations have been challenged at the microscopic level and several additional histological features have been suggested as contributing to MD and FA. To facilitate investigation of the biological underpinnings of DTI parameters, we performed ex-vivo dMRI at 200 μm isotropic resolution on 16 excised meningioma tumor samples. The samples together span a variety of microstructural features: six different meningioma types and two different grades. Diffusion tensor imaging (DTI) was used to produce maps such as MD, FA, in-plane FA (FAIP), axial diffusivity (AD) or radial diffusivity (RD). The maps were coregistered to H&E (hematoxylin & eosin) and VEGF-stained histological slides.
In this repository, we provide raw and analysed DTI maps coregistered to H&E- and VEGF-stained histology slides, as well as an example analysis of the data that aims to quantify the degree to which cell density (CD), structure anisotropy (SA), as determined from histology, in comparison with convolutional neural network (CNN) account for the intra-tumor variability of MD and FAIP in meningioma tumors. The pipeline used to process the raw DTI data and the coregistration tools are hosted by GitHub and the code related to the our example analysis are available here. Please refer and cite our two journal articles mentioned in the section References below for further information on the processing and if you find this data useful. We hope that data can be used in research and education concerning the link between the meningioma microstructure and parameters obtained by diffusion MRI.
Keywords: Radiology, Microstructural features, Mean diffusivity, Fractional anisotropy, cCell density, Cellularity, Meningioma, Coregistration, Hematoxylin & eosin, VEGF.
Sample images with reduced image quality. Please click to preview.
|Cite as||Jan Brabec, Elisabet Englund, Johan Bengzon, Filip Szczepankiewicz, Danielle van Westen, Pia C Sundgren, and Markus Nilsson (2023) Coregistered H&E- and VEGF-stained histology slides with diffusion tensor imaging data at 200 μm resolution in meningioma tumors doi:10.23698/aida/micromen|
|Title||Coregistered H&E- and VEGF-stained histology slides with diffusion tensor imaging data at 200 μm resolution in meningioma tumors|
Danielle van Westen
Pia C Sundgren
|Resolution||Histology slides 0.5 µm ⤫ 0.5 µm. DTI images: 200 µm x 200 µm x 200 µm.|
Bruker 9.4 T BioSpec Avance III MRI scanner
Microscope slide scanner Hamamatsu NanoZoomer S360
The data processed with an in-house DTI pipeline and registration tool available at repositories listed in Kernels
|Stain||Hematoxylin & Eosin (H&E) and VEGF|
|Copyright||Copyright 2023 CC BY 4.0, Markus Nilsson|
Available under the following licenses, described in the License section below.
AIDA BY license
Histology slides coregistered by landmark-based approach with DTI images of meningioma tumor samples.
Histology slides: .tif and .mat files. DTI images: .nii and .mat files.
The pipeline used to process the raw DTI data and the coregistration tools are available at https://github.com/jan-brabec/microimaging_histology_DIB
The code related to the our example analysis are available at https://github.com/jan-brabec/microimaging_vs_histology_in_meningeomas.
Pixel position scaling
Coordinates given are relative to the image width. To get the correct pixel position, X coordinates (and Y coordinates!) should therefore be multiplied with the image width.
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AIDA BY license
Copyright 2023 CC BY 4.0, Markus Nilsson
Permission to use, copy, modify, and/or distribute this data within Analytic Imaging Diagnostics Arena (AIDA) for the purpose of medical diagnostics research with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies, and that publications resulting from the use of this data cite the following works:
Jan Brabec, Elisabet Englund, Johan Bengzon, Filip Szczepankiewicz, Danielle van Westen, Pia C Sundgren, and Markus Nilsson (2023) Coregistered H&E- and VEGF-stained histology slides with diffusion tensor imaging data at 200 μm resolution in meningioma tumors doi:10.23698/aida/micromen.
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