Dataset DOI: 10.5061/dryad.573n5tbqp

Principal Investigator Contact Information:

Carlos M. Rinaldi-Ramos

Institution: University of Florida

Email: [carlos.rinaldi@ufl.edu]

Description of the data and file structure

This dataset supports the publication "Flash nanoprecipitation of magnetic particle imaging tracers with tunable performance". This dataset includes TEM images used in analysis of the iron oxide nanoparticles and the nanocomposite tracers, dynamic light scattering data of nanocomposites, and MPI data. The MPI data includes RELAX measurements, reporting the signal intensity and FWHM of each nanocomposite tracer, and 2D MPI images of select formulations under select imaging conditions. This also includes 3D in vivo images of mice with tracers injected intravenously. 

Files and variables

File: Data_for_Dryad.zip

Description: All the data for the manuscript is inside this zip file.

Structure:

Inside the main folders, there are folders labelled for each figure or table in the main text and supplementary information. All the data for that figure or supplementary figure is in those folders. Within these folders, the data is separated by data type, for example, 2D MPI images, 3D MPI images, RELAX scans, TEM images, CT images, and DLS Dynapro files. The values used to make plots for each figure are located in a CSV labelled "FigureX_panelX" as applicable, where X is the corresponding identifier of the figure and panel.

In the root folder "Data for Dryad", there is a CSV called "Naming Scheme". This file contains any other names used to identify each sample with the formulation conditions under which the sample was made, as well as the iron concentration measured for each sample after formulation. 

Note, Figure S7, Table S1, and Table S2 do not have folders, as the data for those is already reported. The data for Figure S7 is the same as Figure 4, but was just windowed to a different level in Figure S7. The tables S1 and S2 already contain all the data for those.

Please also note that unless otherwise stated, all numerical values are provided exactly as exported by the corresponding instrumentation software. The displayed decimal places do not necessarily represent the true significant figures, precision or accuracy of the measurements.

Folder: Figure 1

Figure 1 in the related manuscript shows data related to the size, both hydrodynamic and physical, of the formulated nanocarriers.

This folder contains 1 sub-folder, named "TEM composite nanoparticles". This folder contains two sub-folders, one for the 0 mg/mL poly(lactic-co-glycolic) acid (PLGA) formulation and one for the 10 mg/mL PLGA formulation, where TEM images in TIF format can be found. Samples were imaged on a FEI Talos F200i S/TEM at 200 kV and up to 120kx magnification.

The CSV called "Figure1_panelA" contains data used to generate the plot in panel A, which contains hydrodynamic diameter histograms for select formulations. The CSV called "Figure1_panelB" contains data used to generate the plot in panel Bwhich contains hydrodynamic diameter histograms for select formulations. The CSV called "Figure1_panelC" contains data used to generate the plot in panel C, which contains the hydrodynamic diameters of each formulation. Hydrodynamic diameter reported is intensity weighted, measured from 100 uL total volume comprised of sample dispersed in water, in the Dynapro Plate Reader III using the dynamic light scattering function. All diameters are reported in nanometers [nm].

Folder: Figure 2

Fiugre 2 contains data relating to MPI performance of the formulated nanocarriers. Figure 2A plots signal intensity and full-width at half maximum (FWHM) in mT for each tracer as a function of concentration of PLGA added. Figure 2B contains linescans obtained by running RELAX scans of select samples. Figure 2C shows 2D MPI images of select samples. Figure 2D contains images and linescans of two select samples.

This folder contains 3 folders for this figure separated by scan type:

The folder MPI 2D contains the images shown in figure 2 panel C, which are the sharpened collinear dicom files from each 2D scan acquired on the Momentum MPI scanner with software MI Momentum v2022.0.1.

The MPI Relax folder contains all the RELAX data for every sample in the manuscript. The negative scans are reported here as those were used to generate the data in Figure 2 panel A. To normalize the RELAX scans to iron mass, take the volume reported in the RELAX scan CSV for each sample and multiply by the concentration of iron reported in the CSV "Naming Scheme" for the corresponding sample.

The Resolution Phantom folder contains the scans used to determine resolution of the two chosen formulations. The two images in this folder are named with the sample identifier followed by "4p5" or "4p75" which corresponds to the distance of separation between the two samples ("4p5" = 4.5 mm; "4.75" = 4.75 mm).

The data for figure 2 panel A is also found in the CSV "Figure2_panelA". The CSV "Figure2_panelB" contains the relax scans used to generate the linescan plot for that panel, acquired under the same conditions as previously described.The CSV "Figure2_panelD" contains the linescan data plotted in panelD for each sample and each distance. 

Folder: Figure 3

The CSV named "Figure3_panelB" contains data for panel B for the 1x scale formulation and the 5x formulation DLS data, acquired as previously described above on the DynaPro Plate Reader III light dynamic scattering function. The CSV named "Figure3_panelC" contains RELAX data for the 1x and 5x formulation data, acquired as stated above.

Folder: Figure 4

Figure 4 shows 3D MPI scans of a mouse overlaid with the skeleton for that mouse. To obtain these images, animals first undergo a 3D MPI scan on the Momentum X-space MPI scanner followed immediately by a CT scan in the IVIS SpectrumCT. This folder contains two folders, Formulation A and Formulation B, that contain 3D MPI scans and CT scans of two mice, one in each folder, that were injected with tracers. The dicom volumes in each folder were exported from 3D slicer after uploading the original sharpened collinear dicom for MPI and CT, cropping the CT to remove the scanning bed, and aligning the MPI and CT volumes using a transformation matrix. The transfomration matrix was generated using a reference MPI and CT image containing capillary landmarks used to do affine landmark registration in 3D Slicer of the 2 volumes.

Formulation A: 10 mg mL⁻¹ PLGA

Formulation B: 0 mg mL⁻¹ PLGA

Folder: Figure 5

Figure 5A shows a calibration curve of two formulations at different iron masses graphed with their signal intensity. Figure 5B is an image showing mixtures of the two particle formulations. Figure 2C shows an image of mixtures in different locations in a 3D printed mouse phantom.

This folder contains two folders. The first, Mixtures, contains the MPI images of mixtures of Formulations A and B at different excitation amplitudes. The naming of these files is "ColorMPI_XX_0000" where XX corresponds to the radio frequency amplitude in mT used for each scan.

The Mouse Phantom folder contains files labelled "Color_Scan1_XXXX_0000" which are the 2D dicom images acquired of the mouse phantom at the different RFA, where XXXX corresponds to the RFA. For example, Color_Scan1_1010_0000 was scanned at an amplitude of 10 mT. The folder Mouse Phantom/Mouse Phantom Registered contains the 2D MPI and 3D CT volumes that have been registered, shown in Figure 5 panel C. These were aligned using similar methods to those described above where a transformation matrix was created by aligning reference images from the MPI and CT using affine landmark registration in 3D Slicer, then applied to the two volumes used in the image and the images were then exported as dicom files. The folder Mouse Phantom/Calibration Samples contains 2D sharpened collinear dicom files from MPI scans of the two formulations at different excitation amplitudes and iron masses. The naming scheme for these files follows "ParticleZ_ref_XX_0000_YYug". Here, Z is replaced with either A or B according to which formulation was used, XX corresponds to the RFA used, for example 10 corresponds to 10 mT, and YY reports the mass of iron used in the sample.

The CSV "Figure5_panelA" contains the maximum signal taken from the 2D MPI images at each excitation amplitude for each formulation. The CSV "Figure5_panelB" contains the linescan data used in the plot in panel B.

Folder: Figure S1

This folder contains a folder called "TEM MNPs" that contains TIF format photos of iron oxide nanoparticle cores. Samples were imaged on a FEI Talos F200i S/TEM at 200 kV and up to 120kx magnification.

The CSV file "FigureS1" contains analyzed diameters from the TEM photos and bins used to generate the histogram in figure S1.

Folder: Figure S2

This folder contains the CSV "FigureS2" where signal intensity and FWHM are reported for each sample (0, 0.5, 1, and 10 mg/mL PLGA) used to generate this figure. 

Folder: Figure S3

This folder contains the CSV "FigureS3" where signal intensity is reported for each sample used to generate this figure. Sample IDs correspond to the IDs in the CSV file "Naming scheme" within the root folder.

Folder: Figure S4

This folder contains the CSV file "FigureS4" where FWHM is reported for each sample used to generate this figure. Sample IDs correspond to the IDs in the CSV file "Naming scheme" within the root folder.

Folder: Figure S5

This folder contains the CSV file "FigureS5" where signal intensity and FWHM are reported for each sample used to generate this figure. Sample IDs correspond to the IDs in the CSV file "Naming scheme" within the root folder.

Folder: Figure S6

This folder contains 2 folders, corresponding to two different samples, each of which was measured at different distances. Folder "FNP_050525_1" corresponds to the sample formulated with 0 mg/mL PLGA and contains DICOM photos of MPI scans performed in the resolution phantom at different fixed distances. The folder "FNP_050525_7" corresponds to the sample formulated with 10 mg/mL PLGA and contains DICOM photos of MPI scans performed in the resolution phantom at different fixed distances. The names of the files in the folders follows "FNP050525_X_YYYY_0000", where X is the sample identifier, and YYYY follows the form 4p75 which would correspond to 4.75 mm of separation.

The CSV file "FNP_050525_1" contains the numerical data used to plot the linescan for each distance for the 0 mg/mL PLGA sample, and the other CSV file "FNP_050525_7" is for the 10 mg/mL PLGA formulation.

Folder: Table S3

This folder contains the CSV file "TableS3" containing average signal intensity and FWHM (mT) at different PLGA mass values from 0 to 10 mg/mL. It also contains coefficients of variance (%) for signal intensity and FWHM as reported in Table S3.