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

Sample images with reduced image quality. Please click to preview.

Dataset information

Short name MICROMEN
Origin Clinical
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
Field Radiology
Organ Brain
Age span
Title Coregistered H&E- and VEGF-stained histology slides with diffusion tensor imaging data at 200 μm resolution in meningioma tumors
Author Jan Brabec
Elisabet Englund
Johan Bengzon
Filip Szczepankiewicz
Danielle van Westen
Pia C Sundgren
Markus Nilsson
Year 2023
DOI doi:10.23698/aida/micromen
Status Completed
Version 1.0.0
Scans 16
Annotations 0
Size 390.06GB
Resolution Histology slides 0.5 µm ⤫ 0.5 µm. DTI images: 200 µm x 200 µm x 200 µm.
Modality MR
Scanner 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
Phase
References
Copyright Copyright 2023 Lund University, Markus Nilsson
Access

Available under the following licenses, described in the License section below.

Controlled access
Free for use in legal and ethical medical diagnostics research.

AIDA BY license
Free for use within AIDA with attribution and co-authorship.

Annotation

Histology slides coregistered by landmark-based approach with DTI images of meningioma tumor samples.

File formats

Histology slides: .tif and .mat files. DTI images: .nii and .mat files.

Kernels

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.

File formats

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.

License

Controlled access

Free for use in legal and ethical medical diagnostics research. Please contact the dataset provider for terms of access.

You are invited to send an access request email from your institutional account.

Clicking the access request email link above should open a draft email message in a new window, to help you provide relevant information for efficient request evaluation. If the above link does not work for you, then please click to view the suggested email text.

AIDA BY license

Copyright 2023 Lund University, 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.

THE DATA IS PROVIDED “AS IS” AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS DATA INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR CHARACTERISTICS OF THIS DATA.