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Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3-Ex vivo
Kurt G Schilling1,2, Amy F D Howard3,4, Francesco Grussu5,6
1Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
Abstract:
Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages that facilitate high spatial resolution and high SNR images, cutting-edge diffusion contrasts, and direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work concludes a three-part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre-processing, data processing, and comparisons with microscopy. In each section, we attempt to provide guidelines and recommendations but also highlight areas for which no guidelines exist (and why), and where future work should lie. We end by providing guidelines on code sharing and data sharing and point toward open-source software and databases specific to small animal and ex vivo imaging.
Insights
This study provides best practices for ex vivo diffusion MRI (dMRI) in preclinical research. It covers image processing, data analysis, and comparisons with microscopy for enhanced tissue microstructure and connectivity studies.
Area of Science:
- Neuroimaging
- Biomedical Engineering
- Microscopy
Background:
- Preclinical diffusion MRI (dMRI) is valuable for methods development, biological characterization, and comparative anatomy.
- Ex vivo dMRI offers advantages like high spatial resolution, high signal-to-noise ratio (SNR), advanced diffusion contrasts, and direct histological validation.
- However, ex vivo dMRI presents unique challenges in tissue preparation, imaging, processing, and interpretation compared to in vivo studies.
Purpose of the Study:
- To provide a comprehensive set of recommendations and considerations for performing ex vivo dMRI on preclinical tissue.
- To outline best practices for image pre-processing, data processing, and comparisons with microscopy in ex vivo dMRI.
- To identify areas lacking established guidelines and suggest future research directions.
Main Methods:
- Review and synthesis of current practices in ex vivo dMRI for preclinical research.
- Focus on image pre-processing steps specific to ex vivo samples.
- Detailed discussion on data processing pipelines and comparison strategies with microscopy.
Main Results:
- Established guidelines for ex vivo dMRI image pre-processing and data analysis.
- Highlighted critical differences and considerations compared to in vivo dMRI protocols.
- Identified knowledge gaps and areas requiring further investigation in ex vivo dMRI methodology.
Conclusions:
- This work offers crucial guidance for optimizing ex vivo dMRI experiments in preclinical settings.
- Emphasizes the importance of standardized protocols for accurate tissue microstructure and connectivity analysis.
- Promotes data and code sharing through open-source platforms for advancing the field.
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