DOI: 10.5061/dryad.jm63xsjmj
title: Data from: On the partial volume effect in magnetic particle imaging

description: This dataset contains raw and processed data used to evaluate the partial
 volume effect (PVE) in magnetic particle imaging (MPI), an emerging
 tomographic imaging modality that visualizes superparamagnetic iron oxide
 nanoparticle (SPION) distributions with high sensitivity and quantitative
 accuracy. The dataset includes raw MPI images in NRRD and DICOM formats,
 optical images of scanned phantoms in TIFF format, and processed Excel
 files with quantitative analyses. Data were obtained using Feraheme and
 VivoTrax+ tracers scanned with various phantom geometries (prisms,
 cylinders, and capillaries) and characteristic sizes. Additional
 experiments included scans of VivoTrax+ phantoms across multiple
 concentrations and at two independent sites. MPI image processing was
 performed using a reported Wiener filter, with outputs such as signal
 recovery coefficients, signal-to-noise ratios, and voxel-based
 reconstructions. The dataset is organized by model geometry and includes
 both raw data and processed results, enabling analysis of signal
 distribution, peak and plateau signal values, and image resolution
 effects. Researchers can use these data to study the PVE in MPI, evaluate
 the impact of finite resolution on signal quantification, and develop
 methods to sharpen MPI images or correct for PVEs. The files are
 compatible with standard data visualization and analysis tools such as
 3DSlicer, Horos, and MATLAB, while Excel files are ready for direct
 interpretation. This dataset has broader relevance for advancing
 quantitative imaging techniques in MPI and beyond by providing insights
 into the influence of object size and shape on imaging accuracy. The
 dataset is provided for non-commercial scientific purposes.
description: Data were collected using magnetic particle imaging (MPI)
 scanners to evaluate the partial volume effect (PVE) in imaging
 superparamagnetic iron oxide nanoparticle (SPION) distributions. Two
 tracers, Feraheme and VivoTrax+, were imaged in 3D-printed phantoms of
 varying geometries and sizes, including prisms, cylinders, and
 capillaries. MPI scans were conducted under controlled conditions at two
 independent sites (University of Florida and Magnetic Insight, Inc.).
 Additional experiments included imaging phantoms with varying tracer
 concentrations. A Wiener filter was applied to process select images of
 VivoTrax+ phantoms to enhance resolution. Quantitative analyses were
 performed to estimate signal recovery coefficients, signal-to-noise
 ratios, image size, and voxel-based signal distributions.
description: # On the partial volume effect in magnetic particle imaging ######
 Principal Investigator Contact Information ``` Name: Carlos M.
 Rinaldi-Ramos Institution: University of Florida Email:
 carlos.rinaldi@ufl.edu ``` ###### Alternate Contact Information ``` Name:
 Hayden J. Good Institution: University of Florida Email:
 hayden.good34@gmail.com ``` ## Dataset Overview This dataset supports the
 publication "On the Partial Volume Effect in Magnetic Particle
 Imaging" and includes data on tracer concentration, image-object size
 relationships, and iron estimation accuracy in magnetic nanoparticle
 studies. The experiments examine the partial volume effect (PVE) in
 Magnetic Particle Imaging (MPI) and include raw imaging data, STL files of
 3D printed models used and the sample bed designed to hold them, optical
 photos of filled models prior to MPI measurement, and processed meta-data
 used in the publication. ### Dates of Data Collection Data was collected
 from the summer of 2023 until the spring of 2024. ### Funding This work
 was supported by the National Institute for Biomedical Imaging and
 Bioengineering under award number R01EB031224, the National Cancer
 Institute under award number R21CA26353, and the National Institute of
 Neurological Disorders and Stroke under award number R21NS125089. ## Data
 Sources All data were derived from MPI imaging samples collected from 2023
 - 2024 by the authors. ### Recommended Citation Good, Hayden J. et al. On
 the partial volume effect in magnetic particle imaging. Physics in
 Medicine and Biology. In review. 2024. ## Description of the data and file
 structure Multiple files in this repository are .csv, .dcm, and .nrrd file
 types. Users are not provided with the appropriate scripts to analyze the
 raw imaging date due to proprietal information; however, users are
 provided with the file outputs. Some csv files have NaNs, which were
 created accidentally during xlsx to csv conversion and have no
 significance to the data. Their presence simply means that there was a gap
 in the data that was filled. ### Acronyms and important naming ``` HS -
 High sensitivity (scan mode) HR - High resolution (Scan mode) Std -
 Standard (scan mode) RC - Recovery Coefficient FWHM - Full-width at
 half-maximum Native - 'Native' and minimally processed scan data
 Sharpened - 'Sharpened' processed scan data Wiener Filter -
 Native data that was transformed through a Wiener filter ``` ### Parent
 folder structure ##### 10mmX Prisms - Feraheme These files are associated
 with rectangular prism models with fixed x dimension of 10mm and variable
 dimension of z dimension filled with tracer solution of Feraheme. #####
 10mmX Prisms - Vivotrax+ These files are associated with rectangular prism
 models with fixed x dimension of 10mm and variable dimension of z
 dimension filled with tracer solution of Vivotrax+. ##### 10mmX Prisms -
 MI These files are associated with rectangular prism models with fixed x
 dimension of 10mm and variable dimension of z dimension filled with tracer
 solution of Vivotrax+, filled and imaged at Magnetic Insight campus. #####
 5mmX Prisms These files are associated with rectangular prism models with
 fixed x dimension of 5mm and variable dimension of z dimension filled with
 tracer solution of Vivotrax+. ##### 15mmX Prisms These files are
 associated with rectangular prism models with fixed x dimension of 15mm
 and variable dimension of z dimension filled with tracer solution of
 Vivotrax+. ##### Cylinders These files are associated with cylindrical
 models with varying x and z (radial) dimensions filled with tracer
 solution of Vivotrax+. ##### Small Cylinders These files are associated
 with capillary tubing with varying x and z (radial) dimensions filled with
 tracer solution of Vivotrax+. ##### Empty Bed scans These files are
 associated with empty bore scans of the MOMENTUM scanner. ##### \[Fe]
 Cylinders These files are associated with a set of 14mm Diameter cylinder
 models filled with carying concentrations of Vivotrax+. ##### \[Fe] Prisms
 These files are associated with a set of 14x10mm rectangular prism models
 filled with carying concentrations of Vivotrax+. ##### RELAX Scans These
 files are associated with the RELAX relaxometry output of the UF MOMENTUM
 Scanner for both Vivotrax+ and Feraheme batches used for scans. ##### STL
 files for models These files are STL files for the models used in the
 study. ### Model specific folder structure Most model folders listed above
 have the following format: ##### DICOM Native These are the
 'native' imaging data in DICOM format from the MOMENTUM scanner
 associated with the model specific folder. ##### Nrrd Native These are the
 'native' imaging data in NRRD format from the MOMENTUM scanner
 associated with the model specific folder. ##### DICOM Sharpened These are
 the 'sharpened' imaging data in DICOM format from the MOMENTUM
 scanner associated with the model specific folder. ##### Nrrd Sharpened
 These are the 'sharpened' imaging data in NRRD format from the
 MOMENTUM scanner associated with the model specific folder. ##### Excel
 files These are the excel files of processed meta data used in the
 manuscript. Sheets are ##### CSV files These are the same excel files and
 sheets of processed meta data used in the manuscript ##### Photos These
 are the optical photos taken from the MOMENTUM MPI scanner prior to the
 model being scanned. ### Description of file names ##### MPI output names
 Each DICOM and NRRD file is formatted where the first three numbers are
 the scan number of the day, followed by scan mode (HS - High sensitivity,
 HR - High resolution, Std - Standard), followed by user interface (AUI -
 advanced user interface (this means the data had extra processing. this
 data was not presented in the manuscript), SUI - Standard user interface
 (this data was published)), and finally the model variable identifier. For
 example, 004_HS_SUI_30mm.dcm refers to the 4th scan of the day, performed
 in High sensitivity scan mode using the standard user interface, and the
 30mm model of the parent model (in this case the author was using the
 10mmX Prisms - Feraheme model folder as an example). ##### Excel file
 format The file begins with the original MPI folder format (may not match
 published folder name) associated with the data, then a descriptor of what
 is in the excel file. Descriptors include Full scan data (digitized full
 data set in excel sheet), Linescans (extracted line scans of interest from
 the full scan data), and RC 2x2mm (recovery coefficient data calculations
 where the center of the model was found and statistics regarding the
 center was extracted). If the file name includes "HS" it was
 scanned under high sensitivity mode; if not, it was scanned under Std
 mode. ##### CSV file format The CSV files are simply extractions of the
 Excel files listed above in a format that does not require Microsoft
 software to load. ### Description of Excel file naming #### Full Scan data
 Each sheet refers to the model name (Std_SUI_30mm is the 30mm model
 scanned under Std SUI settings) #### Linescan Results ##### Z-scans Auto
 This sheet refers to the linescans (automatically found) in the z
 direction. The first column is the imaging spacing dimensions, and the
 following columns are specific to each model. ##### Z-scans Manual This
 sheet refers to the linescans (manually selected) in the z direction. The
 first column is the imaging spacing dimensions, and the following columns
 are specific to each model. ##### X-scans Auto This sheet refers to the
 linescans (automatically found) in the x direction. The first column is
 the imaging spacing dimensions, and the following columns are specific to
 each model. ##### X-scans Manual This sheet refers to the linescans
 (manually selected) in the x direction. The first column is the imaging
 spacing dimensions, and the following columns are specific to each model.
 ##### FWHMzs or FWHMxs This sheet refers to the calculated Full-width at
 half-maximums (FWHMs) of the linescans from the above models, and the FWHM
 of several linescans adjacent to the central FHWM. #### RC 2x2mm This data
 depicts the center of each model. the extracted center is shown in the
 table, then the mean, stdev, and maximum of the matrix of data are
 provided. the Sheets are associated with the scan mode and model. ####
 Others There are some unique excel files that are self-explanatory. If any
 questions arise, please contact either primary author.