Correction of z-motion artefacts to allow population imaging of synaptic activity in behaving mice.
ABSTRACT: KEY POINTS:Motion artefacts associated with motor behaviour are an inevitable problem of multiphoton imaging in awake behaving animals, particularly when imaging synapses. Correction of axial motion artefacts usually requires volumetric imaging resulting in slower rates of acquisition. We describe a method to correct z-motion artefacts that is easy to implement and allows population imaging of synaptic activity while scanning a single plane in a standard multiphoton microscope. The method uses a reference volume acquired in two colour channels - an activity reporter and an anatomical marker of blood vessels. The procedure estimates the z-displacement in every frame and applies an intensity correction in which the z intensity profile for each synapse is modelled as a Moffat function. We demonstrate that the method allows synaptic calcium signals to be collected from populations of synaptic boutons in mouse primary visual cortex during locomotion. ABSTRACT:Functional imaging of head-fixed, behaving mice using two-photon imaging of fluorescent activity reporters has become a powerful tool for studying the function of the brain. Motion artefacts are an inevitable problem during such experiments and are routinely corrected for in x and y dimensions. However, axial (z) shifts of several microns can also occur, leading to intensity fluctuations in structures such as synapses that are small compared to the axial point-spread function of the microscope. Here we present a simple strategy to correct z-motion artefacts arising over the course of a time-series experiment in a single optical plane. Displacement in z was calculated using dye-filled blood vessels as an anatomical marker, providing high contrast images and accuracy to within ?0.1 µm. The axial profiles of ROIs corresponding to synapses were described using a Moffat function and this 'ROI-spread function' used to correct activity traces on an ROI-by-ROI basis. We demonstrate the accuracy and utility of the procedures in simulation experiments using fluorescent beads and then apply them to correcting measurements of synaptic activity in populations of vasoactive-intestinal peptide (VIP) interneurons expressing the synaptic reporter SyGCaMP6f. Correction of z-motion artefacts had a substantial impact on the apparent correlation between synaptic activity and running speed, demonstrating the importance of correcting these when performing imaging experiments in awake mice.
Project description:Positron Emission Tomography (PET) images are prone to motion artefacts due to the long acquisition time of PET measurements. Recently, simultaneous magnetic resonance imaging (MRI) and PET have become available in the first generation of Hybrid MR-PET scanners. In this work, the elimination of artefacts due to head motion in PET neuroimages is achieved by a new approach utilising MR-based motion tracking in combination with PET list mode data motion correction for simultaneous MR-PET acquisitions. The method comprises accurate MR-based motion measurements, an intra-frame motion minimising and reconstruction time reducing temporal framing algorithm, and a list mode based PET reconstruction which utilises the Ordinary Poisson Algorithm and avoids axial and transaxial compression. Compared to images uncorrected for motion, an increased image quality is shown in phantom as well as in vivo images. In vivo motion corrected images show an evident increase of contrast at the basal ganglia and a good visibility of uptake in tiny structures such as superior colliculi.
Project description:Temporal focusing multiphoton microscopy (TFMPM) has the advantage of area excitation in an axial confinement of only a few microns; hence, it can offer fast three-dimensional (3D) multiphoton imaging. Herein, fast volumetric imaging via a developed digital micromirror device (DMD)-based TFMPM has been realized through the synchronization of an electron multiplying charge-coupled device (EMCCD) with a dynamic piezoelectric stage for axial scanning. The volumetric imaging rate can achieve 30 volumes per second according to the EMCCD frame rate of more than 400 frames per second, which allows for the 3D Brownian motion of one-micron fluorescent beads to be spatially observed. Furthermore, it is demonstrated that the dynamic HiLo structural multiphoton microscope can reject background noise by way of the fast volumetric imaging with high-speed DMD patterned illumination.
Project description:We describe a cardiac gated high in-plane resolution axial human cervical spinal cord diffusion tensor imaging (DTI) protocol. Multiple steps were taken to optimize both image acquisition and image processing. The former includes slice-by-slice cardiac triggering and individually tiltable slices. The latter includes (i) iterative 2D retrospective motion correction, (ii) image intensity outlier detection to minimize the influence of physiological noise, (iii) a non-linear DTI estimation procedure incorporating non-negative eigenvalue priors, and (iv) tract-specific region-of-interest (ROI) identification based on an objective geometry reference. Using these strategies in combination, radial diffusivity (?(?)) was reproducibly measured in white matter (WM) tracts (adjusted mean [95% confidence interval]=0.25 [0.22, 0.29] ?m(2)/ms), lower than previously reported ?(?) values in the in vivo human spinal cord DTI literature. Radial diffusivity and fractional anisotropy (FA) measured in WM varied from rostral to caudal as did mean translational motion, likely reflecting respiratory motion effect. Given the considerable sensitivity of DTI measurements to motion artifact, we believe outlier detection is indispensable in spinal cord diffusion imaging. We also recommend using a mixed-effects model to account for systematic measurement bias depending on cord segment.
Project description:Diffusion tensor imaging (DTI) is particularly suitable for kidney studies due to tubules, collector ducts and blood vessels in the medulla that produce spatially restricted diffusion of water molecules, thus reflecting the high grade of anisotropy detectable by DTI. Kidney DTI is still a challenging technique where the off-resonance susceptibility artefacts and subject motion can severely affect the reproducibility of results. The aim of this study is to design a reliable processing pipeline by assessing different image processing approaches in terms of reproducibility and image artefacts correction. The results of four different processing pipelines (eddy: correction of eddy-currents and motion between DTI volume; eddy-s2v: eddy and within DTI volume motion correction; topup: eddy and geometric distortion correction; topup-s2v: topup and within DTI volume motion correction) are compared in terms of reproducibility by test-retest analysis in 14 healthy subjects. Within-subject coefficient of variation (wsCV) and intra-class correlation coefficient (ICC) are measured to assess the reproducibility and Dice similarity index is evaluated for the spatial alignment between DTI and anatomical images. Topup-s2v pipeline provides highest reproducibility (wsCV = 0.053, ICC = 0.814) and best correction of image distortion (Dice = 0.83). This study definitely provides a recipe for data processing, enabling for a clinical suitability of kidney DTI.
Project description:Motion correction in PET has become more important as system resolution has improved. The purpose of this study was to evaluate the accuracy of event-by-event and frame-based MC methods in human brain PET imaging.Motion compensated image reconstructions were performed with static and dynamic simulated high resolution research tomograph data with frame-based image reconstructions, using a range of measured human head motion data. Image intensities in high-contrast regions of interest (ROI) and parameter estimates in tracer kinetic models were assessed to evaluate the accuracy of the motion correction methods.Given accurate motion data, event-by-event motion correction can reliably correct for head motions. The average ROI intensities and the kinetic parameter estimates VT and BPND were comparable to the true values. The frame-based motion correction methods with correctly aligned attenuation map using the average of externally acquired motion data or motion data derived from image registration give comparable quantitative accuracy. For large intraframe (>5 mm) motion, the frame-based methods produced ≈ 9% bias in ROI intensities, ≈ 5% in VT, and ≈ 10% in BPND estimates. In addition, in real studies that lack a ground truth, the normalized weighted residual sum of squared difference is a potential figure-of-merit to evaluate the accuracy of motion correction methods.The authors conclude that frame-based motion correction methods are accurate when the intraframe motion is less than 5 mm and when the attenuation map is accurately aligned. Given accurate motion data, event-by-event motion correction can reliably correct for head motion in human brain PET studies.
Project description:PURPOSE:When using simultaneous multi-slice (SMS) EPI for background suppressed (BGS) arterial spin labeling (ASL), correction of through-plane motion could introduce artefacts, because the slices with most effective BGS are adjacent to slices with the least BGS. In this study, a new framework is presented to correct for such artefacts. METHODS:The proposed framework consists of 3 steps: (1) homogenization of the static tissue signal over the different slices to eliminate most inter-slice differences because of different levels of BGS, (2) application of motion correction, and (3) extraction of a perfusion-weighted signal using a general linear model. The proposed framework was evaluated by simulations and a functional ASL study with intentional head motion. RESULTS:Simulation studies demonstrated that the strong signal differences between slices with the most and least effective BGS caused sub-optimal estimation of motion parameters when through-plane motion was present. Although use of the M0 image as the reference for registration allowed 82% improvement of motion estimation for through-plane motion, it still led to residual subtraction errors caused by different static tissue signal between control and label because of different BGS levels. By using our proposed framework, those problems were minimized, and the accuracy of CBF estimation was improved. Moreover, the functional ASL study showed improved detection of visual and motor activation when applying the framework as compared to conventional motion correction, as well as when motion correction was completely omitted. CONCLUSION:When combining BGS-ASL with SMS-EPI, particular attention is needed to avoid artefacts introduced by motion correction. With the proposed framework, these issues are minimized.
Project description:OBJECTIVES: The aim of this study was to assess artefacts and their impact on cone beam CT (CBCT) image quality (IQ) after head motion simulated by a robot skull. METHODS: A fully dentate human skull incorporated into a robot simulated pre-determined patient movements. Ten head motion patterns were selected based on the movement of the C-arm of the CBCT units (no motion as reference). Three CBCT units were used [a three-dimensional eXam (K) (KaVo Dental GmbH, Biberach, Germany), a Promax 3D MAX (P) (Planmeca Oy, Helsinki, Finland) and a Scanora(®) 3D (S) (Soredex Oy, Tuusula, Finland)]. Axial images were qualitatively assessed at three levels: mental foramen (MF), infraorbital foramen and supraorbital foramen, and artefacts characterized as stripe-like, double contours, unsharpness or ring-like. A 100 mm visual analogue scale (VAS) was used to quantitatively assess IQ. Cross-sectional images of the lower third molar and MF bilaterally were also evaluated by VAS. Four blinded examiners assessed the images. RESULTS: For all units and motion patterns, stripe-like artefacts were the most common. The four observers agreed on the presence of at least one artefact type in 90% of the images. Axial images showed lower overall IQ after motion (VAS = 72.4 ± 24.0 mm) than reference images (VAS = 97.3 ± 2.6 mm). The most severe artefacts were seen at the MF level. For cross-sectional images, IQ was lowest after tremor. The mean IQ range was 74-89 and 57-90 for isolated (tilting, rotation and nodding) and combined (nodding + tilting and rotation + tilting) movements, respectively. IQ for MF was lower than for third molar for any movement except tremor. CONCLUSIONS: Head motion of any type resulted in artefacts in CBCT images. The impact on IQ depended on the region and level in the skull.
Project description:BACKGROUND AND PURPOSE:The superior soft-tissue contrast of 4D-T2w MRI motivates its use for delineation in radiotherapy treatment planning. We address current limitations of slice-selective implementations, including thick slices and artefacts originating from data incompleteness and variable breathing. MATERIALS AND METHODS:A method was developed to calculate midposition and 4D-T2w images of the whole thorax from continuously acquired axial and sagittal 2D-T2w MRI (1.5?×?1.5?×?5.0?mm3). The method employed image-derived respiratory surrogates, deformable image registration and super-resolution reconstruction. Volunteer imaging and a respiratory motion phantom were used for validation. The minimum number of dynamic acquisitions needed to calculate a representative midposition image was investigated by retrospectively subsampling the data (10-30 dynamic acquisitions). RESULTS:Super-resolution 4D-T2w MRI (1.0?×?1.0?×?1.0?mm3, 8 respiratory phases) did not suffer from data incompleteness and exhibited reduced stitching artefacts compared to sorted multi-slice MRI. Experiments using a respiratory motion phantom and colour-intensity projection images demonstrated a minor underestimation of the motion range. Midposition diaphragm differences in retrospectively subsampled acquisitions were <1.1?mm compared to the full dataset. 10 dynamic acquisitions were found sufficient to generate midposition MRI. CONCLUSIONS:A motion-modelling and super-resolution method was developed to calculate high quality 4D/midposition T2w MRI from orthogonal 2D-T2w MRI.
Project description:High-resolution diffusion MRI can provide the ability to resolve small brain structures, enabling investigations of detailed white matter architecture. A major challenge for in vivo high-resolution diffusion MRI is the low signal-to-noise ratio. In this work, we combine two highly compatible methods, ultra-high field and three-dimensional multi-slab acquisition to improve the SNR of high-resolution diffusion MRI. As each kz plane is encoded using a single-shot echo planar readout, scan speeds of the proposed technique are similar to the commonly used two-dimensional diffusion MRI. In-plane parallel acceleration is applied to reduce image distortions. To reduce the sensitivity of auto-calibration signal data to subject motion and respiration, several new adaptions of the fast low angle excitation echo-planar technique (FLEET) that are suitable for 3D multi-slab echo planar imaging are proposed and evaluated. A modified reconstruction scheme is proposed for auto-calibration with the most robust method, Slice-FLEET acquisition, to make it compatible with navigator correction of motion induced phase errors. Slab boundary artefacts are corrected using the nonlinear slab profile encoding method recently proposed by our group. In vivo results demonstrate that using 7T and three-dimensional multi-slab acquisition with improved auto-calibration signal acquisition and nonlinear slab boundary artefacts correction, high-quality diffusion MRI data with ~1mm isotropic resolution can be achieved.
Project description:PURPOSE:To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs. MATERIALS AND METHODS:The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison. RESULTS:The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P < 0.01) and volume overlap and distance between region boundaries measures were significantly improved (P < 0.01). CONCLUSION:The proposed approach to align MRI time series enables more accurate quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs. LEVEL OF EVIDENCE:1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:403-412.