ANHIR: Automatic Non-Rigid Histological Image Registration Challenge.
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ABSTRACT:
SUBMITTER: Borovec J
PROVIDER: S-EPMC7584382 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:[18F]fluoro-2-deoxy-D-glucose ([18F]FDG) positron emission tomography (PET) is a valuable tool for monitoring response to therapy in oncology. In longitudinal studies, however, patients are not scanned in exactly the same position. Rigid and non-rigid image registration can be applied in order to reuse baseline volumes of interest (VOI) on consecutive studies of the same patient. The purpose of this study was to investigate the impact of various image registration strategies on standardized uptake value (SUV) and metabolic volume test-retest variability (TRT). METHODS:Test-retest whole-body [18F]FDG PET/CT scans were collected retrospectively for 11 subjects with advanced gastrointestinal malignancies (colorectal carcinoma). Rigid and non-rigid image registration techniques with various degrees of locality were applied to PET, CT, and non-attenuation corrected PET (NAC) data. VOI were drawn independently on both test and retest scans. VOI drawn on test scans were projected onto retest scans and the overlap between projected VOI and manually drawn retest VOI was quantified using the Dice similarity coefficient (DSC). In addition, absolute (unsigned) differences in TRT of SUVmax, SUVmean, metabolic volume and total lesion glycolysis (TLG) were calculated in on one hand the test VOI and on the other hand the retest VOI and projected VOI. Reference values were obtained by delineating VOIs on both scans separately. RESULTS:Non-rigid PET registration showed the best performance (median DSC: 0.82, other methods: 0.71-0.81). Compared with the reference, none of the registration types showed significant absolute differences in TRT of SUVmax, SUVmean and TLG (p > 0.05). Only for absolute TRT of metabolic volume, significant lower values (p < 0.05) were observed for all registration strategies when compared to delineating VOIs separately, except for non-rigid PET registrations (p = 0.1). Non-rigid PET registration provided good volume TRT (7.7%) that was smaller than the reference (16%). CONCLUSION:In particular, non-rigid PET image registration showed good performance similar to delineating VOI on both scans separately, and with smaller TRT in metabolic volume estimates.
| S-EPMC3349514 | biostudies-literature
Project description:To confirm the fully automated rigid image registration (A-RIR) accuracy in postoperative spine stereotactic body radiation therapy (SBRT), we conducted a multicenter non-inferiority study compared to the human rigid image registration (H-RIR). Twenty-eight metastatic cancer patients who underwent postoperative spine SBRT are enrolled-image registration (IR) of planning computed tomography (CT) and CT-myelogram for delineating the spinal cord. The adopted A-RIR workflow is a contour-focused algorithm performing a rigid registration by maximizing normalized mutual information (NMI) restricted to the data contained within the automatically extracted contour. Three radiation oncologists (ROs) from multicenters were prompted to review two blinded registrations and choose one for clinical use. Indistinguishable cases were allowed to vote equivalent, counted A-RIR side. A-RIR is considered non-inferior to H-RIR if the lower limit of the 95% confidence interval (CI) of A-RIR preferable/equivalent is greater than 0.45. We also evaluated the NMI improvement from the baseline and the translational/rotational errors between A-RIR and H-RIR. The A-RIR preferable/equivalent was selected in 21 patients (0.75, 95% CI: 0.55-0.89), demonstrating non-inferiority to H-RIR. The A-RIR's NMI improvement was greater than H-RIR in 24 patients: the mean value ± SD was 0.225 ± 0.115 in A-RIR and 0.196 ± 0.114 in H-RIR (P < 0.001). The absolute translational error was 0.38 ± 0.31 mm. The rotational error was -0.03 ± 0.20, 0.05 ± 0.19, -0.04 ± 0.20 degrees in axial, coronal, and sagittal planes (range: -0.66-0.52). In conclusion, A-RIR shows non-inferior to H-RIR in CT and CT-myelogram registration for postoperative spine SBRT planning.
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Project description:Registration of three-dimensional ultrasound (3DUS) volumes is necessary in several applications, such as when stitching volumes to expand the field of view or when stabilizing a temporal sequence of volumes to cancel out motion of the probe or anatomy. Current systems that register 3DUS volumes either use external tracking systems (electromagnetic or optical), which add expense and impose limitations on acquisitions, or are image-based methods that operate offline and are incapable of providing immediate feedback to clinicians. This paper presents a real-time image-based algorithm for rigid registration of 3DUS volumes designed for acquisitions in which small probe displacements occur between frames. Described is a method for feature detection and descriptor formation that takes into account the characteristics of 3DUS imaging. Volumes are registered by determining a correspondence between these features. A global set of features is maintained and integrated into the registration, which limits the accumulation of registration error. The system operates in real-time (i.e. volumes are registered as fast or faster than they are acquired) by using an accelerated framework on a graphics processing unit. The algorithm's parameter selection and performance is analyzed and validated in studies which use both water tank and clinical images. The resulting registration accuracy is comparable to similar feature-based registration methods, but in contrast to these methods, can register 3DUS volumes in real-time.
| S-EPMC3267836 | biostudies-literature
Project description:Accurate and robust non-rigid registration of pre-procedure magnetic resonance (MR) imaging to intra-procedure trans-rectal ultrasound (TRUS) is critical for image-guided biopsies of prostate cancer. Prostate cancer is one of the most prevalent forms of cancer and the second leading cause of cancer-related death in men in the United States. TRUS-guided biopsy is the current clinical standard for prostate cancer diagnosis and assessment. State-of-the-art, clinical MR-TRUS image fusion relies upon semi-automated segmentations of the prostate in both the MR and the TRUS images to perform non-rigid surface-based registration of the gland. Segmentation of the prostate in TRUS imaging is itself a challenging task and prone to high variability. These segmentation errors can lead to poor registration and subsequently poor localization of biopsy targets, which may result in false-negative cancer detection. In this paper, we present a non-rigid surface registration approach to MR-TRUS fusion based on a statistical deformation model (SDM) of intra-procedural deformations derived from clinical training data. Synthetic validation experiments quantifying registration volume of interest overlaps of the PI-RADS parcellation standard and tests using clinical landmark data demonstrate that our use of an SDM for registration, with median target registration error of 2.98 mm, is significantly more accurate than the current clinical method. Furthermore, we show that the low-dimensional SDM registration results are robust to segmentation errors that are not uncommon in clinical TRUS data.
| S-EPMC5514316 | biostudies-literature
Project description:BackgroundHigh resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions such as tissue tearing, folding and missing at each slide. Performing registration for the whole tissue slices may be adversely affected by distorted tissue regions. Consequently, regional registration is found to be more effective. In this paper, we propose a new approach to an accurate and robust registration of regions of interest for whole slide images. We introduce the idea of multi-scale attention for registration.ResultsUsing mean similarity index as the metric, the proposed algorithm (mean ± SD [Formula: see text]) followed by a fine registration algorithm ([Formula: see text]) outperformed the state-of-the-art linear whole tissue registration algorithm ([Formula: see text]) and the regional version of this algorithm ([Formula: see text]). The proposed algorithm also outperforms the state-of-the-art nonlinear registration algorithm (original: [Formula: see text], regional: [Formula: see text]) for whole slide images and a recently proposed patch-based registration algorithm (patch size 256: [Formula: see text] , patch size 512: [Formula: see text]) for medical images.ConclusionUsing multi-scale attention mechanism leads to a more robust and accurate solution to the problem of regional registration of whole slide images corrupted in some parts by major histological artifacts in the imaged tissue.
| S-EPMC7718714 | biostudies-literature
Project description:Measurement of cell shortening is an important technique for assessment of physiology and pathophysiology of cardiac myocytes. Many types of heart disease are associated with decreased myocyte shortening, which is commonly caused by structural and functional remodeling. Here, we present a new approach for local measurement of 2-dimensional strain within cells at high spatial resolution. The approach applies non-rigid image registration to quantify local displacements and Cauchy strain in images of cells undergoing contraction. We extensively evaluated the approach using synthetic cell images and image sequences from rapid scanning confocal microscopy of fluorescently labeled isolated myocytes from the left ventricle of normal and diseased canine heart. Application of the approach yielded a comprehensive description of cellular strain including novel measurements of transverse strain and spatial heterogeneity of strain. Quantitative comparison with manual measurements of strain in image sequences indicated reliability of the developed approach. We suggest that the developed approach provides researchers with a novel tool to investigate contractility of cardiac myocytes at subcellular scale. In contrast to previously introduced methods for measuring cell shorting, the developed approach provides comprehensive information on the spatio-temporal distribution of 2-dimensional strain at micrometer scale.
| S-EPMC5031511 | biostudies-literature
Project description:ObjectivesRigid image registration (RIR) and deformable image registration (DIR) are widely used in radiotherapy. This project aims to capture current international approaches to image registration.MethodsA survey was designed to identify variations in use, resources, implementation, and decision-making criteria for clinical image registration. This was distributed to radiotherapy centers internationally in 2018.ResultsThere were 57 responses internationally, from the Americas (46%), Australia/New Zealand (32%), Europe (12%), and Asia (10%). Rigid image registration and DIR were used clinically for computed tomography (CT)-CT registration (96% and 51%, respectively), followed by CT-PET (81% and 47%), CT-CBCT (84% and 19%), CT-MR (93% and 19%), MR-MR (49% and 5%), and CT-US (9% and 0%). Respondent centers performed DIR using dedicated software (75%) and treatment planning systems (29%), with 84% having some form of DIR software. Centers have clinically implemented DIR for atlas-based segmentation (47%), multi-modality treatment planning (65%), and dose deformation (63%). The clinical use of DIR for multi-modality treatment planning and accounting for retreatments was considered to have the highest benefit-to-risk ratio (69% and 67%, respectively).ConclusionsThis survey data provides useful insights on where, when, and how image registration has been implemented in radiotherapy centers around the world. DIR is mainly in clinical use for CT-CT (51%) and CT-PET (47%) for the head and neck (43-57% over all use cases) region. The highest benefit-risk ratio for clinical use of DIR was for multi-modality treatment planning and accounting for retreatments, which also had higher clinical use than for adaptive radiotherapy and atlas-based segmentation.
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Project description:We introduce an end-to-end deep-learning framework for 3D medical image registration. In contrast to existing approaches, our framework combines two registration methods: an affine registration and a vector momentum-parameterized stationary velocity field (vSVF) model. Specifically, it consists of three stages. In the first stage, a multi-step affine network predicts affine transform parameters. In the second stage, we use a U-Net-like network to generate a momentum, from which a velocity field can be computed via smoothing. Finally, in the third stage, we employ a self-iterable map-based vSVF component to provide a non-parametric refinement based on the current estimate of the transformation map. Once the model is trained, a registration is completed in one forward pass. To evaluate the performance, we conducted longitudinal and cross-subject experiments on 3D magnetic resonance images (MRI) of the knee of the Osteoarthritis Initiative (OAI) dataset. Results show that our framework achieves comparable performance to state-of-the-art medical image registration approaches, but it is much faster, with a better control of transformation regularity including the ability to produce approximately symmetric transformations, and combining affine as well as non-parametric registration.
| S-EPMC7286599 | biostudies-literature
Project description:The purpose of this study is to find the uncertainties in the reconstruction of MR compatible ring-tandem intracavitary applicators of high-dose rate image-based brachytherapy treatment planning using rigid registration of 3D MR and CT image fusion. Tandem and ring reconstruction in MR image based brachytherapy planning was done using rigid registration of CT and MR applicator geometries. Verifications of registration for applicator fusion were performed in six verification steps at three different sites of tandem ring applicator set. The first site consists of three errors at the level of ring plane in (1) cranio caudal shift (Cranial Shift) of ring plane along tandem axis, (2) antero-posterior shift (AP Shift) perpendicular to tandem axis on the plane containing the tandem, and (3) lateral shift (Lat Shift) perpendicular to the plane containing the tandem at the level of ring plane. The other two sites are the verifications at the tip of tandem and neck of the ring. The verification at the tip of tandem consists of two errors in (1) antero-posterior shift (AP Shift) perpendicular to tandem axis on the plane containing the tandem, and (2) lateral shift (Lat Shift) perpendicular to the plane containing the tandem. The third site of verification at the neck of the ring is the error due to the rotation of ring about tandem axis. The impact of translational errors from -5 mm to 5 mm in the step of 1 mm along x-, y-, and z-axis and three rotational errors about these axes from -19.1° to 19.1° in the step of 3.28° on dose-volume histogram parameters (D(2cc), D(1cc), D(0.1cc), and D(5cc) of bladder, rectum, and sigmoid, and D90 and D98 of HRCTV were also analyzed. Maximum registration errors along cranio-caudal direction was 2.2 mm (1 case), whereas the errors of 31 out of 34 cases of registration were found within 1.5 mm, and those of two cases were less than 2mm but greater than 1.5 mm. Maximum rotational error of ring about tandem axis was 3.15° (1.1 mm). In other direction and different sites of the ring applicator set, the errors were within 1.5 mm. The impacts of registration errors on DVH parameters of bladder, rectum, and sigmoid were very sensitive to antero-posterior shift. Cranio-caudal errors of registration also largely affected the rectum DVH parameters. Largest change of 17.95% per mm and 20.65% per mm in all the DVH parameters of all OARs and HRCTV were observed for ? and ? rotational errors as compare to other translational and rotational errors. Catheter reconstruction in MR image using rigid registration of applicator geometries of CT and MR images is a feasible technique for MR image-based intracavitary brachytherapy planning. The applicator regis-tration using the contours of tandem and neck of the ring of CT and MR images decreased the rotational error about tandem axis. Verification of CT MR image fusion using applicator registration which consists of six steps of verification at three different sites in ring applicator set can report all the errors due to translation and rotational shift along ?, ?, and ?. ? and ? rotational errors, which produced potential changes in DVH parameters, can be tackled using AP Shift and Lat Shift at the tip of tandem. The maximum shift was still found along the tandem axis in this technique.
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Project description:Digital image analysis is a fundamental component of quantitative microscopy. However, intravital microscopy presents many challenges for digital image analysis. In general, microscopy volumes are inherently anisotropic, suffer from decreasing contrast with tissue depth, lack object edge detail and characteristically have low signal levels. Intravital microscopy introduces the additional problem of motion artefacts, resulting from respiratory motion and heartbeat from specimens imaged in vivo. This paper describes an image registration technique for use with sequences of intravital microscopy images collected in time-series or in 3D volumes. Our registration method involves both rigid and nonrigid components. The rigid registration component corrects global image translations, whereas the nonrigid component manipulates a uniform grid of control points defined by B-splines. Each control point is optimized by minimizing a cost function consisting of two parts: a term to define image similarity, and a term to ensure deformation grid smoothness. Experimental results indicate that this approach is promising based on the analysis of several image volumes collected from the kidney, lung and salivary gland of living rodents.
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