Sensitive and automated detection of iron-oxide-labeled cells using phase image cross-correlation analysis

QSM reconstruction challenge 2.0: A realistic in silico head phantom for MRI data simulation and evaluation of susceptibility mapping procedures

PURPOSE

To create a realistic in silico head phantom for the second QSM reconstruction challenge and for future evaluations of processing algorithms for QSM.

METHODS

We created a digital whole-head tissue property phantom by segmenting and postprocessing high-resolution (0.64 mm isotropic), multiparametric MRI data acquired at 7 T from a healthy volunteer. We simulated the steady-state magnetization at 7 T using a Bloch simulator and mimicked a Cartesian sampling scheme through Fourier-based processing. Computer code for generating the phantom and performing the MR simulation was designed to facilitate flexible modifications of the phantom in the future, such as the inclusion of pathologies as well as the simulation of a wide range of acquisition protocols. Specifically, the following parameters and effects were implemented: TR and TE, voxel size, background fields, and RF phase biases. Diffusion-weighted imaging phantom data are provided, allowing future investigations of tissue-microstructure effects in phase and QSM algorithms.

RESULTS

The brain part of the phantom featured realistic morphology with spatial variations in relaxation and susceptibility values similar to the in vivo setting. We demonstrated some of the phantom's properties, including the possibility of generating phase data with nonlinear evolution over TE due to partial-volume effects or complex distributions of frequency shifts within the voxel.

CONCLUSION

The presented phantom and computer programs are publicly available and may serve as a ground truth in future assessments of the faithfulness of quantitative susceptibility reconstruction algorithms.

Tracking Neural Progenitor Cell Migration in the Rodent Brain Using Magnetic Resonance Imaging

The study of neurogenesis and neural progenitor cells (NPCs) is important across the biomedical spectrum, from learning about normal brain development and studying disease to engineering new strategies in regenerative medicine. In adult mammals, NPCs proliferate in two main areas of the brain, the subventricular zone (SVZ) and the subgranular zone, and continue to migrate even after neurogenesis has ceased within the rest of the brain. In healthy animals, NPCs migrate along the rostral migratory stream (RMS) from the SVZ to the olfactory bulb, and in diseased animals, NPCs migrate toward lesions such as stroke and tumors. Here we review how MRI-based cell tracking using iron oxide particles can be used to monitor and quantify NPC migration in the intact rodent brain, in a serial and relatively non-invasive fashion. NPCs can either be labeled directly in situ by injecting particles into the lateral ventricle or RMS, where NPCs can take up particles, or cells can be harvested and labeled in vitro, then injected into the brain. For in situ labeling experiments, the particle type, injection site, and image analysis methods have been optimized and cell migration toward stroke and multiple sclerosis lesions has been investigated. Delivery of labeled exogenous NPCs has allowed imaging of cell migration toward more sites of neuropathology, which may enable new diagnostic and therapeutic opportunities for as-of-yet untreatable neurological diseases.

Detection of microcalcifications by characteristic magnetic susceptibility effects using MR phase image cross-correlation analysis

PURPOSE

To develop and evaluate a new method for detecting calcium deposits using their characteristic magnetic susceptibility effects on magnetic resonance (MR) images at high fields and demonstrate its potential in practice for detecting breast microcalcifications.

METHODS

Characteristic dipole signatures of calcium deposits were detected in magnetic resonance phase images by computing the cross-correlation between the acquired data and a library of templates containing simulated phase patterns of spherical deposits. The influence of signal-to-noise ratio and various other MR parameters on the results were assessed using simulations and validated experimentally. The method was tested experimentally for detection of calcium fragments within gel phantoms and calcium-like inhomogeneities within chicken tissue at 7 T with optimized MR acquisition parameters. The method was also evaluated for detection of simulated microcalcifications, modeled from biopsy samples of malignant breast cancer, inserted in silico into breast magnetic resonance imaging (MRIs) of healthy subjects at 7 T. For both assessments of calcium fragments in phantoms and biopsy-based simulated microcalcifications in breast MRIs, receiver operator characteristic curve analyses were performed to determine the cross-correlation index cutoff, for achieving optimal sensitivity and specificity, and the area under the curve (AUC), for measuring the method's performance.

RESULTS

The method detected calcium fragments with sizes of 0.14-0.79 mm, 1 mm calcium-like deposits, and simulated microcalcifications with sizes of 0.4-1.0 mm in images with voxel sizes between (0.2 mm)(3) and (0.6 mm)(3). In images acquired at 7 T with voxel sizes of (0.2 mm)(3)-(0.4 mm)(3), calcium fragments (size 0.3-0.4 mm) were detected with a sensitivity, specificity, and AUC of 78%-90%, 51%-68%, and 0.77%-0.88%, respectively. In images acquired with a human 7 T scanner, acquisition times below 12 min, and voxel sizes of (0.4 mm)(3)-(0.6 mm)(3), simulated microcalcifications with sizes of 0.6-1.0 mm were detected with a sensitivity, specificity, and AUC of 75%-87%, 54%-87%, and 0.76%-0.90%, respectively. However, different microcalcification shapes were indistinguishable.

CONCLUSIONS

The new method is promising for detecting relatively large microcalcifications (i.e., 0.6-0.9 mm) within the breast at 7 T in reasonable times. Detection of smaller deposits at high field may be possible with higher spatial resolution, but such images require relatively long scan times. Although mammography can detect and distinguish the shape of smaller microcalcifications with superior sensitivity and specificity, this alternative method does not expose tissue to ionizing radiation, is not affected by breast density, and can be combined with other MRI methods (e.g., dynamic contrast-enhanced MRI and diffusion weighted MRI), to potentially improve diagnostic performance.

Small animal cardiovascular MR imaging and spectroscopy

The use of MR imaging and spectroscopy for studying cardiovascular disease processes in small animals has increased tremendously over the past decade. This is the result of the remarkable advances in MR technologies and the increased availability of genetically modified mice. MR techniques provide a window on the entire timeline of cardiovascular disease development, ranging from subtle early changes in myocardial metabolism that often mark disease onset to severe myocardial dysfunction associated with end-stage heart failure. MR imaging and spectroscopy techniques play an important role in basic cardiovascular research and in cardiovascular disease diagnosis and therapy follow-up. This is due to the broad range of functional, structural and metabolic parameters that can be quantified by MR under in vivo conditions non-invasively. This review describes the spectrum of MR techniques that are employed in small animal cardiovascular disease research and how the technological challenges resulting from the small dimensions of heart and blood vessels as well as high heart and respiratory rates, particularly in mice, are tackled.

Phase-contrast helium-3 MRI of aerosol deposition in human airways

One of the key challenges in the study of health-related aerosols is predicting and monitoring sites of particle deposition in the respiratory tract. The potential health risks of ambient exposure to environmental or workplace aerosols and the beneficial effects of medical aerosols are strongly influenced by the site of aerosol deposition along the respiratory tract. Nuclear medicine is the only current modality that combines quantification and regional localization of aerosol deposition, and this technique remains limited by its spatial and temporal resolutions and by patient exposure to radiation. Recent work in MRI has shed light on techniques to quantify micro-sized magnetic particles in living bodies by the measurement of associated static magnetic field variations. With regard to lung MRI, hyperpolarized helium-3 may be used as a tracer gas to compensate for the lack of MR signal in the airways, so as to allow assessment of pulmonary function and morphology. The extrathoracic region of the human respiratory system plays a critical role in determining aerosol deposition patterns, as it acts as a filter upstream from the lungs. In the present work, aerosol deposition in a mouth-throat phantom was measured using helium-3 MRI and compared with single-photon emission computed tomography. By providing high sensitivity with high spatial and temporal resolutions, phase-contrast helium-3 MRI offers new insights for the study of particle transport and deposition.

Monitoring the effects of dexamethasone treatment by MRI using in vivo iron oxide nanoparticle-labeled macrophages

Introduction

Rheumatoid arthritis (RA) is a chronic disease causing recurring inflammatory joint attacks. These attacks are characterized by macrophage infiltration contributing to joint destruction. Studies have shown that RA treatment efficacy is correlated to synovial macrophage number. The aim of this study was to experimentally validate the use of in vivo superparamagnetic iron oxide nanoparticle (SPION) labeled macrophages to evaluate RA treatment by MRI.

Methods

The evolution of macrophages was monitored with and without dexamethasone (Dexa) treatment in rats. Two doses of 3 and 1 mg/kg Dexa were administered two and five days following induction of antigen induced arthritis. SPIONs (7 mg Fe/rat) were injected intravenously and the knees were imaged in vivo on days 6, 10 and 13. The MR images were scored for three parameters: SPION signal intensity, SPION distribution pattern and synovial oedema. Using 3D semi-automated software, the MR SPION signal was quantified. The efficacy of SPIONs and gadolinium chelate (Gd), an MR contrast agent, in illustrating treatment effects were compared. Those results were confirmed through histological measurements of number and area of macrophages and nanoparticle clusters using CD68 immunostaining and Prussian blue staining respectively.

Results

Results show that the pattern and the intensity of SPION-labeled macrophages on MRI were altered by Dexa treatment. While the Dexa group had a uniform elliptical line surrounding an oedema pocket, the untreated group showed a diffused SPION distribution on day 6 post-induction. Dexa reduced the intensity of SPION signal 50-60% on days 10 and 13 compared to controls (P = 0.00008 and 0.002 respectively). Similar results were found when the signal was measured by the 3D tool. On day 13, the persisting low grade arthritis progression could not be demonstrated by Gd. Analysis of knee samples by Prussian blue and CD68 immunostaining confirmed in vivo SPION uptake by macrophages. Furthermore, CD68 immunostaining revealed that Dexa treatment significantly decreased the area and number of synovial macrophages. Prussian blue quantification corresponded to the macrophage measurements and both were in agreement with the MRI findings.

Conclusions

We have demonstrated the feasibility of MRI tracking of in vivo SPION-labeled macrophages to assess RA treatment effects.

In vivo quantification of SPIO nanoparticles for cell labeling based on MR phase gradient images

Along with the development of modern imaging technologies, contrast agents play increasingly important roles in both clinical applications and scientific research. Super-paramagnetic iron oxide (SPIO) nanoparticles, a negative contrast agent, have been extensively used in magnetic resonance imaging (MRI), such as in vivo labeling and tracking of cells. However, there still remain many challenges, such as in vivo quantification of SPIO nanoparticles. In this work, an MR phase gradient-based method was proposed to quantify the SPIO nanoparticles. As a calibration, a phantom experiment using known concentrations (10, 25, 50, 100, 150 and 250 µg/ml) of SPIO was first conducted to verify the proposed quantification method. In a following in vivo experiment, C6 glioma cells labeled with SPIO nanoparticles were implanted into flanks of four mice, which were scanned 1-3 days post-injection for in vivo quantification of SPIO concentration. The results showed that the concentration of SPIO nanoparticles could be determined in both phantom and in vivo experiments using the developed MR phase gradients approach.

MR phase imaging: sensitive and contrast-enhancing visualization in cellular imaging

The successful translation of stem-cell therapies requires a detailed understanding of the fate of transplanted cells. Magnetic resonance imaging (MRI) has provided a noninvasive means of imaging cell dynamics in vivo by prelabeling cell with T(2) shortening iron oxide particles. However, this approach suffers from a gradual loss of sensitivity since active cell mitosis could decrease the cellular contrast agent (CA) concentration below detection level. In addition, the interpretation of images may be confounded by hypointensities induced by factors other than this CA susceptibility effect (CASE). We therefore examined the feasibility of exploiting the phase information in MRI to increase the sensitivity of cellular imaging and to differentiate the CASE from endogenous image hypointensity. Phase aliasing and the B(0) field inhomogeneity effect were removed by applying a reliable unwrapping algorithm and a high-pass filter, respectively, thus delineating phase variations originating from high spatial frequencies due to the CASE. We found that the filtered phase map detects labeled cells with high sensitivity and can readily differentiate the cell migration track from the white matter, both of which are hypointense in T(2)-weighted magnitude images. Furthermore, an approximate fivefold contrast-to-noise ratio enhancement can be achieved with an MRI phase map over conventional T(2)-weighted magnitude images.

Assessment of cell infiltration in myocardial infarction: a dose-dependent study using micrometer-sized iron oxide particles

Myocardial infarction (MI) is a leading cause of death and disabilities. Inflammatory cells play a vital role in the process of postinfarction remodeling and repair. Inflammatory cell infiltration into the infarct site can be monitored using T 2-weighted MRI following an intravenous administration of iron oxide particles. In this study, various doses of micrometer-sized iron oxide particles (1.1-14.5 μg Fe/g body weight) were injected into the mouse blood stream before a surgical induction of MI. Cardiac MRIs were performed at 3, 7, 14, and 21 days postinfarction to monitor the signal attenuation at the infarct site. A dose-dependent phenomenon of signal attenuation was observed at the infarct site, with a higher dose leading to a darker signal. The study suggests an optimal temporal window for monitoring iron oxide particles-labeled inflammatory cell infiltration to the infarct site using MRI. The dose-dependent signal attenuation also indicates an optimal iron oxide dose of approximately 9.1-14.5 μg Fe/g body weight. A lower dose cannot differentiate the signal attenuation, whereas a higher dose would cause significant artifacts. This iron oxide-enhanced MRI technique can potentially be used to monitor cell migration and infiltration at the pathological site or to confirm any cellular response following some specific treatment strategies.

Automated detection and characterization of SPIO-labeled cells and capsules using magnetic field perturbations

Understanding how individual cells behave inside living systems will help enable new diagnostic tools and cellular therapies. Superparamagnetic iron oxide particles can be used to label cells and theranostic capsules for noninvasive tracking using MRI. Contrast changes from superparamagnetic iron oxide are often subtle relative to intrinsic sources of contrast, presenting a detection challenge. Here, we describe a versatile postprocessing method, called Phase map cross-correlation Detection and Quantification (PDQ), that automatically identifies localized deposits of superparamagnetic iron oxide, estimating their volume magnetic susceptibility and magnetic moment. To demonstrate applicability, PDQ was used to detect and characterize superparamagnetic iron oxide-labeled magnetocapsules implanted in porcine liver and suspended in agarose gel. PDQ was also applied to mouse brains infiltrated by MPIO-labeled macrophages following traumatic brain injury; longitudinal, in vivo studies tracked individual MPIO clusters over 3 days, and tracked clusters were corroborated in ex vivo brain scans. Additionally, we applied PDQ to rat hearts infiltrated by MPIO-labeled macrophages in a transplant model of organ rejection. PDQ magnetic measurements were signal-to-noise ratio invariant for images with signal-to-noise ratio > 11. PDQ can be used with conventional gradient-echo pulse sequences, requiring no extra scan time. The method is useful for visualizing biodistribution of cells and theranostic magnetocapsules and for measuring their relative iron content.

A novel method for quantitative monitoring of transplanted islets of langerhans by positive contrast magnetic resonance imaging

The Automatic Quantitative Ultrashort Echo Time imaging (AQUTE) protocol for serial MRI allows quantitative in vivo monitoring of iron labeled pancreatic islets of Langerhans transplanted into the liver, quantifying graft implantation and persistence in a rodent model. Rats (n = 14), transplanted with iron oxide loaded cells (0-4000 islet equivalents, IEQ), were imaged using a 3D radial ultrashort echo time difference technique (dUTE) on a Siemens MAGNETOM 3T clinical scanner up to 5 months postsurgery. In vivo 3D dUTE images gave positive contrast from labeled cells, suppressing liver signal and small vessels, allowing automatic quantification. Position of labeled islet clusters was consistent over time and quantification of hyperintense pixels correlated with the number of injected IEQs (R² = 0.898, p < 0.0001), and showed persistence over time (5 months posttransplantation). Automatic quantification was superior to standard imaging and manual counting methods, due to the uniform suppressed background and high contrast, resulting in significant timesavings, reproducibility and ease of quantification. Three-dimensional coverage of the whole liver in the absence of cardiac/respiratory artifact provided further improvement over conventional imaging. This imaging protocol reliably quantifies transplanted islet mass and has high translational potential to clinical studies of transplanted pancreatic islets.

Positive contrast technique for the detection and quantification of superparamagnetic iron oxide nanoparticles in MRI

In vivo detection and quantification of cells labeled with superparamagnetic iron oxide (SPIO) nanoparticles has been attracting increasing attention. In particular, positive contrast methods, such as susceptibility gradient mapping (SGM) and phase gradient mapping (PGM), have been proposed for the improved detection of SPIO nanoparticles. In this study, a different implementation of the PGM method is introduced; it calculates the phase gradient in the image space using a fast Fourier transform without the need for phase unwrapping. We first compared positive contrast generation between the PGM and SGM methods, which estimates the susceptibility gradient in k space through echo shift measurements. Next, PGM was applied to quantify SPIO concentrations by fitting the resulting phase gradient maps to those of a theoretical model. MR experiments were conducted using a 3-T magnet scanner to acquire two datasets: the first was acquired from a gelatin phantom with three SPIO-doped vials of different concentrations, and the second was obtained in vivo from a nude rat with SPIO-labeled C6 glioma cells implanted in the flanks. The sensitivity of the PGM and SGM methods was compared using various factors, including different SPIO concentrations, TEs and signal-to-noise ratios. Based on the theoretical model of an infinite cylinder, the results demonstrated that, without loss of spatial resolution, the PGM method presents positive contrast maps with a higher sensitivity than SGM at medium and low SPIO concentrations, whereas SGM is more sensitive than PGM at longer TEs. The quantification of SPIO concentrations using the phantom dataset was also reported. On the basis of the same infinite cylinder model, it was shown that the PGM method provides an accurate estimation of SPIO concentration.

Serial monitoring of endogenous neuroblast migration by cellular MRI

Endogenous neural progenitor cell migration in vivo can be monitored using MRI-based cell tracking. The current protocol is that micron sized iron oxide particles (MPIOs) are injected into the lateral ventricle proximal to the neural stem cell niche in the brain. MPIOs are endocytosed and incorporated into the neural progenitor cell population, making them visible by gradient echo MRI. Here this new method is extended to serially quantify cell migration. Initially, in vivo cell labeling methodologies were optimized, as high susceptibility effects from the MPIOs generate substantial signal loss around the injection site, masking early migratory events. Then, using improved labeling conditions, a longitudinal study was conducted over two weeks to quantify the migration of labeled progenitor cells toward the olfactory bulb (OB). By 3 days following injection, we calculated 0.26% of the volume of the OB containing labeled cells. By 8days, this volume nearly doubled to 0.49% and plateaued. These MRI results are in accordance with our data on iron quantification from the OB and with those from purely immunohistochemical studies.

Quantification of SPIO nanoparticles in vivo using the finite perturber method

The susceptibility gradients generated by super-paramagnetic iron oxide (SPIO) nanoparticles make them an ideal contrast agent in magnetic resonance imaging. Traditional quantification methods for SPIO nanoparticle-based contrast agents rely on either mapping T₂* values within a region or by modeling the magnetic field inhomogeneities generated by the contrast agent. In this study, a new model-based SPIO quantification method is introduced. The proposed method models magnetic field inhomogeneities by approximating regions containing SPIOs as ensembles of magnetic dipoles, referred to as the finite perturber method. The proposed method was verified using data acquired from a phantom and in vivo mouse models. The phantom consisted of an agar solution with four embedded vials, each vial containing known but different concentrations of SPIO nanoparticles. Gaussian noise was also added to the phantom data to test performance of the proposed method. The in vivo dataset was acquired using five mice, each of which was subcutaneously implanted in the flanks with 1 × 10(5) labeled and 1 × 10(6) unlabeled C6 glioma cells. For the phantom data set, the proposed algorithm was generate accurate estimations of the concentration of SPIOs. For the in vivo dataset, the method was able to give estimations of the concentration within SPIO-labeled tumors that are reasonably close to the known concentration.

Optimization of iron oxide nanoparticle detection using ultrashort echo time pulse sequences: comparison of T1, T2*, and synergistic T1- T2* contrast mechanisms

Iron oxide nanoparticles (IONPs) are used in various MRI applications as negative contrast agents. A major challenge is to distinguish regions of signal void due to IONPs from those due to low signal tissues or susceptibility artifacts. To overcome this limitation, several positive contrast strategies have been proposed. Relying on IONP T(1) shortening effects to generate positive contrast is a particularly appealing strategy because it should provide additional specificity when associated with the usual negative contrast from effective transverse relaxation time (T(2)*) effects. In this article, ultrashort echo time imaging is shown to be a powerful technique which can take full advantage of both contrast mechanisms. Methods of comparing T(1) and T(2)* contrast efficiency are described and general rules that allow optimizing IONP detection sensitivity are derived. Contrary to conventional wisdom, optimizing T(1) contrast is often a good strategy for imaging IONPs. Under certain conditions, subtraction of a later echo signal from the ultrashort echo time signal not only improves IONP specificity by providing long T(2)* background suppression but also increases detection sensitivity, as it enables a synergistic combination of usually antagonist T(1) and T(2)* contrasts. In vitro experiments support our theory, and a molecular imaging application is demonstrated using tumor-targeted IONPs in vivo.

Iron quantification of microbleeds in postmortem brain

Brain microbleeds (BMB) are associated with chronic and acute cerebrovascular disease and present a source of pathologic iron to the brain proportional to extravasated blood. Therefore, BMB iron content is potentially a valuable biomarker. We tested noninvasive phase image methods to quantify iron content and estimate true source diameter (i.e., unobscured by the blooming effect) of BMB in postmortem human tissue. Tissue slices containing BMB were imaged using a susceptibility weighted imaging protocol at 11.7T. BMB lesions were assayed for iron content using atomic absorption spectrometry. Measurements of geometric features in phase images were related to lesion iron content and source diameter using a mathematical model. BMB diameter was estimated by image feature geometry alone without explicit relation to the magnetic susceptibility. A strong linear relationship (R(2) = 0.984, P < 0.001) predicted by theory was observed in the experimental data, presenting a tentative standardization curve where BMB iron content in similar tissues could be calculated. In addition, we report BMB iron mass measurements, as well as upper bound diameter and lower bound iron concentration estimates. Our methods potentially allows the calculation of brain iron load indices based on BMB iron content and classification of BMB by size unobscured by the blooming effect.

SWIFT detection of SPIO-labeled stem cells grafted in the myocardium

We report initial results from studies using sweep imaging with Fourier transformation (SWIFT) to detect superparamagnetic iron oxide (SPIO) particle-labeled stem cells in the rat heart. In experiments performed on phantoms containing titanium balls or SPIO-labeled cells, frequency-shifted signals surrounding the paramagnetic objects produced a pileup artifact visualized by SWIFT. Total signal intensity was retained to a much greater extent by SWIFT as compared to gradient echo imaging. SWIFT imaging of excised and in vivo hearts showed (a) reduced blooming artifact as compared with gradient echo imaging, which helped reduce ambiguity in the detection of SPIO-labeled cells; (b) enhancement of off-resonance signals relative to the background in the imaginary component of images; and (c) detailed myocardial anatomy in magnitude images, which provided anatomic reference. These features suggest SWIFT can facilitate the detection of SPIO-laden cells in the cardiovascular system.

Quantification of punctate iron sources using magnetic resonance phase

Iron-mediated tissue damage is present in cerebrovascular and neurodegenerative diseases and neurotrauma. Brain microbleeds are often present in these maladies and are assuming increasing clinical importance. Because brain microbleeds present a source of pathologic iron to the brain, the noninvasive quantification of this iron pool is potentially valuable. Past efforts to quantify brain iron have focused on content estimation within distributed brain regions. In addition, conventional approaches using "magnitude" images have met significant limitations. In this study, a technique is presented to quantify the iron content of punctate samples using phase images. Samples are modeled as magnetic dipoles and phase shifts due to local dipole field perturbations are mathematically related to sample iron content and radius using easily recognized geometric features in phase images. Phantoms containing samples of a chitosan-ferric oxyhydroxide composite (which serves as a mimic for hemosiderin) were scanned with a susceptibility-weighted imaging sequence at 11.7 T. Plots relating sample iron content and radius to phase image features were compared to theoretical predictions. The primary result is the validation of the technique by the excellent agreement between theory and the iron content plot. This research is a potential first step toward quantification of punctate brain iron sources such as brain microbleeds.

Quantification of SPIO nanoparticles using phase gradient mapping

A new method is developed to quantify the concentration of super-paramagnetic iron oxide (SPIO) contrast agent using magnetic resonance imaging (MRI). The proposed method utilizes a positive contrast method, known as phase gradient mapping (PGM), to find the gradient of the field map. Then the concentration is calculated by fitting the gradient of the field map to the gradient of an ideal geometric model. The proposed method was compared to relaxivity-based SPIO quantification method and was applied to calculate the concentration of SPIO contrast agent for MRI experiments performed on a phantom with known concentrations. The results obtained from the proposed method accord well with the true concentrations.

Detection and quantification of magnetically labeled cells by cellular MRI

Labeling cells with superparamagnetic iron oxide (SPIO) nanoparticles, paramagnetic contrast agent (gadolinium) or perfluorocarbons allows for the possibility of tracking single or clusters of labeled cells within target tissues following either direct implantation or intravenous injection. This review summarizes the practical issues regarding detection and quantification of magnetically labeled cells with various MRI contrast agents with a focus on SPIO nanoparticles.