A dual micro-CT system for small animal imaging

Badea, Cristian T.; Johnston, S. M.; Johnson, Ben; Lin, Ming De; Hedlund, Laurence W.; Johnson, G. Allan

doi:10.1117/12.772303

Cited by 54 publications

(72 citation statements)

References 16 publications

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“…An intravascular catheter (24 ga, BD Medical Systems, Sandy, UT) was inserted in the lateral tail vein to inject a liposomal blood pool contrast agent ([10], [11]; 0.30 ml/g with 135 mg Iodine/ml; half-life ~40 hours). X-ray projections were acquired with one chain of our dual tube/detector micro-CT system [12]. 342 projections (size: 1002x667, pixel size: 88 μm) were acquired per phase for a total scanning time of approximately 40 minutes per mouse (4 minutes/phase, 10 phases).…”

Section: In Vivo Mouse Experimentsmentioning

confidence: 99%

Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications

et al. 2013

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A number of investigators have demonstrated the potential of preclinical micro-CT in characterizing cardiovascular disease in mouse models. One major hurdle to advancing this approach is the extensive user interaction required to derive quantitative metrics from these 4D image arrays (space + time). In this work, we present: (1) a method for constructing an average anatomic cardiac atlas of the mouse based on 4D micro-CT images, (2) a fully automated approach for segmenting newly acquired cardiac data sets using the atlas, and (3) a quantitative characterization of atlasbased segmentation accuracy and consistency. Employing the deformable registration toolkit, ANTs, the construction of minimal deformation fields, and a novel adaptation of joint bilateral filtration, our atlas construction scheme was used to integrate 6, C57BL/6 cardiac micro-CT data sets, reducing the noise standard deviation from ~70 HU in the individual data sets to ~21 HU in the atlas data set. Using the segmentation tools in Atropos and our atlas-based segmentation, we were able to propagate manual labels to 5, C57BL/6 data sets not used in atlas construction. Average Dice coefficients and volume accuracies (respectively) over phases 1 (ventricular diastole), 3, and 5 (ventricular systole) of these 5 data sets were as follows: left ventricle, 0.96, 0.96; right ventricle, 0.89, 0.92; left atrium, 0.88, 0.89; right atrium, 0.86, 0.92; myocardium, 0.90, 0.94. Once the atlas was constructed and segmented, execution of the proposed automated segmentation scheme took ~6.5 hours per data set, versus more than 50 hours required for a manual segmentation.

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Section: In Vivo Mouse Experimentsmentioning

confidence: 99%

Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications

et al. 2013

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“…23, is used to a acquire anatomical micro-CT data. The system has two Varian A197 x-ray tubes with dual focal spots ͑0.6 and 1.0 mm͒.…”

Section: Micro-ct Systemmentioning

confidence: 99%

Three-dimensional reconstruction in free-space whole-body fluorescence tomography of mice using optically reconstructed surface and atlas anatomy

2009

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Abstract. We present a 3-D image reconstruction method for freespace fluorescence tomography of mice using hybrid anatomical prior information. Specifically, we use an optically reconstructed surface of the experimental animal and a digital mouse atlas to approximate the anatomy of the animal as structural priors to assist image reconstruction. Experiments are carried out on a cadaver of a nude mouse with a fluorescent inclusion ͑2.4-mm-diam cylinder͒ implanted in the chest cavity. Tomographic fluorescence images are reconstructed using an iterative algorithm based on a finite element method. Coregistration of the fluorescence reconstruction and micro-CT ͑computed tomography͒ data acquired afterward show good localization accuracy ͑localization error 1.2± 0.6 mm͒. Using the optically reconstructed surface, but without the atlas anatomy, image reconstruction fails to show the fluorescent inclusion correctly. The method demonstrates the utility of anatomical priors in support of free-space fluorescence tomography.

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“…12 An algorithm for 4D cardiac micro-CT segmentation using histogram and region sampling technique was previously proposed. 13 The method yielded consistent functional measurements for the left ventricle but it was not readily applicable to the myocardium and the other chambers of the heart. Another example of segmentation of 4D cardiac gated micro-CT images of the mouse is to make manual segmentation first in one phase and then propagate to other phases via registration.…”

Section: B 4d Image Segmentation In Other Areasmentioning

confidence: 99%

“…The disadvantage of this approach is that much labor is required for building the 4D atlas. The second category is to adopt registration related techniques [11][12][13][14][16][17][18][19] which are the common approaches for 4D image segmentation by performing segmentation individually in each 3D volume. A 4D image is segmented by first manually carrying out segmentation of a 3D spatial volume corresponding to one time point (TP) and then propagating the manual segmentation to other time points to achieve segmentations at those time points.…”

Section: B 4d Image Segmentation In Other Areasmentioning

confidence: 99%

Minimally interactive segmentation of 4D dynamic upper airway MR images via fuzzy connectedness

et al. 2016

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Purpose: There are several disease conditions that lead to upper airway restrictive disorders. In the study of these conditions, it is important to take into account the dynamic nature of the upper airway. Currently, dynamic magnetic resonance imaging is the modality of choice for studying these diseases. Unfortunately, the contrast resolution obtainable in the images poses many challenges for an effective segmentation of the upper airway structures. No viable methods have been developed to date to solve this problem. In this paper, the authors demonstrate a practical solution by employing an iterative relative fuzzy connectedness delineation algorithm as a tool. Methods: 3D dynamic images were collected at ten equally spaced instances over the respiratory cycle (i.e., 4D) in 20 female subjects with obstructive sleep apnea syndrome. The proposed segmentation approach consists of the following steps. First, image background nonuniformities are corrected which is then followed by a process to correct for the nonstandardness of MR image intensities. Next, standardized image intensity statistics are gathered for the nasopharynx and oropharynx portions of the upper airway as well as the surrounding soft tissue structures including air outside the body region, hard palate, soft palate, tongue, and other soft structures around the airway including tonsils (left and right) and adenoid. The affinity functions needed for fuzzy connectedness computation are derived based on these tissue intensity statistics. In the next step, seeds for fuzzy connectedness computation are specified for the airway and the background tissue components. Seed specification is needed in only the 3D image corresponding to the first time instance of the 4D volume; from this information, the 3D volume corresponding to the first time point is segmented. Seeds are automatically generated for the next time point from the segmentation of the 3D volume corresponding to the previous time point, and the process continues and runs without human interaction and completes in 10 s for segmenting the airway structure in the whole 4D volume. Results: Qualitative evaluations performed to examine smoothness and continuity of motions of the entire upper airway as well as its transverse sections at critical anatomic locations indicate that the segmentations are consistent. Quantitative evaluations of the separate 200 3D volumes and the 20 4D volumes yielded true positive and false positive volume fractions around 95% and 0.1%, respectively, and mean boundary placement errors under 0.5 mm. The method is robust to variations in the subjective action of seed specification. Compared with a segmentation approach based on a registration technique to propagate segmentations, the proposed method is more efficient, accurate, and less prone to error propagation from one respiratory time point to the next. Conclusions: The proposed method is the first demonstration of a viable and practical approach for segmenting the upper airway structures in dynamic MR images. Compared to ...

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A dual micro-CT system for small animal imaging

Cited by 54 publications

References 16 publications

Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications

Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications

Three-dimensional reconstruction in free-space whole-body fluorescence tomography of mice using optically reconstructed surface and atlas anatomy

Minimally interactive segmentation of 4D dynamic upper airway MR images via fuzzy connectedness

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