Spectroscopic imaging with single acquisition ptychography and a hyperspectral detector

We present a new method of single acquisition spectroscopic imaging with high spatial resolution. The technique is based on the combination of polychromatic synchrotron radiation and ptychographic imaging with a recently developed energy discriminating detector. We demonstrate the feasibility with a Ni-Cu test sample recorded at I13-1 of the Diamond Light Source, UK. The two elements can be clearly distinguished and the Ni absorption edge is identified. The results prove the feasibility of obtaining high-resolution structural and chemical images within a single acquisition using a polychromatic X-ray beam. The capability of resolving the absorption edge applies to a wide range of research areas, such as magnetic domains imaging and element specific investigations in biological, materials, and earth sciences. The method utilises the full available radiation spectrum and is therefore well suited for broadband radiation sources

X-Ray ptychography with a laboratory source

X-ray ptychography has revolutionized nanoscale phase contrast imaging at large-scale synchrotron sources in recent years. We present here the first successful demonstration of the technique in a small-scale laboratory setting. An experiment was conducted with a liquid metal jet x-ray source and a single photon-counting detector with a high spectral resolution. The experiment used a spot size of 5 mu m to produce a ptychographic phase image of a Siemens star test pattern with a submicron spatial resolution. The result and methodology presented show how high-resolution phase contrast imaging can now be performed at small-scale laboratory sources worldwide

Towards a framework for analysis of eye-tracking studies in the three dimensional environment: a study of visual search by experienced readers of endoluminal CT colonography.

Objective: Eye tracking in three dimensions is novel, but established descriptors derived from two-dimensional (2D) studies are not transferable. We aimed to develop metrics suitable for statistical comparison of eye-tracking data obtained from readers of three-dimensional (3D) “virtual” medical imaging, using CT colonography (CTC) as a typical example. Methods: Ten experienced radiologists were eye tracked while observing eight 3D endoluminal CTC videos. Sub-sequently, we developed metrics that described their visual search patterns based on concepts derived from 2D gaze studies. Statistical methods were developed to allow analysis of the metrics. Results: Eye tracking was possible for all readers. Visual dwell on the moving region of interest (ROI) was defined as pursuit of the moving object across multiple frames. Using this concept of pursuit, five categories of metrics were defined that allowed characterization of reader gaze behaviour. These were time to first pursuit, identi-fication and assessment time, pursuit duration, ROI size and pursuit frequency. Additional subcategories allowed us to further characterize visual search between readers in the test population. Conclusion: We propose metrics for the characterization of visual search of 3D moving medical images. These metrics can be used to compare readers’ visual search patterns and provide a reproducible framework for the analysis of gaze tracking in the 3D environment. Advances in knowledge: This article describes a novel set of metrics that can be used to describe gaze behaviour when eye tracking readers during interpretation of 3D medical images. These metrics build on those established for 2D eye tracking and are applicable to increasingly common 3D medical image displays

CT colonography: external clinical validation of an algorithm for computer-assisted prone and supine registration

Purpose To perform external validation of a computer-assisted registration algorithm for prone and supine computed tomographic (CT) colonography and to compare the results with those of an existing centerline method. Materials and Methods All contributing centers had institutional review board approval; participants provided informed consent. A validation sample of CT colonographic examinations of 51 patients with 68 polyps (6–55 mm) was selected from a publicly available, HIPAA compliant, anonymized archive. No patients were excluded because of poor preparation or inadequate distension. Corresponding prone and supine polyp coordinates were recorded, and endoluminal surfaces were registered automatically by using a computer algorithm. Two observers independently scored three-dimensional endoluminal polyp registration success. Results were compared with those obtained by using the normalized distance along the colonic centerline (NDACC) method. Pairwise Wilcoxon signed rank tests were used to compare gross registration error and McNemar tests were used to compare polyp conspicuity. Results Registration was possible in all 51 patients, and 136 paired polyp coordinates were generated (68 polyps) to test the algorithm. Overall mean three-dimensional polyp registration error (mean ± standard deviation, 19.9 mm ± 20.4) was significantly less than that for the NDACC method (mean, 27.4 mm ± 15.1; P = .001). Accuracy was unaffected by colonic segment (P = .76) or luminal collapse (P = .066). During endoluminal review by two observers (272 matching tasks, 68 polyps, prone to supine and supine to prone coordinates), 223 (82%) polyp matches were visible (120° field of view) compared with just 129 (47%) when the NDACC method was used (P < .001). By using multiplanar visualization, 48 (70%) polyps were visible after scrolling ± 15 mm in any multiplanar axis compared with 16 (24%) for NDACC (P < .001). Conclusion Computer-assisted registration is more accurate than the NDACC method for mapping the endoluminal surface and matching the location of polyps in corresponding prone and supine CT colonographic acquisitions

Endoluminal surface registration for CT colonography using Haustral Fold Matching

Computed Tomographic (CT) colonography is a technique used for the detection of bowel cancer or potentially precancerous polyps. The procedure is performed routinely with the patient both prone and supine to differentiate fixed colonic pathology from mobile faecal residue. Matching corresponding locations is difficult and time consuming for radiologists due to colonic deformations that occur during patient repositioning. We propose a novel method to establish correspondence between the two acquisitions automatically. The problem is first simplified by detecting haustral folds using a graph cut method applied to a curvature-based metric applied to a surface mesh generated from segmentation of the colonic lumen. A virtual camera is used to create a set of images that provide a metric for matching pairs of folds between the prone and supine acquisitions. Image patches are generated at the fold positions using depth map renderings of the endoluminal surface and optimised by performing a virtual camera registration over a restricted set of degrees of freedom. The intensity difference between image pairs, along with additional neighbourhood information to enforce geometric constraints over a 2D parameterisation of the 3D space, are used as unary and pair-wise costs respectively, and included in a Markov Random Field (MRF) model to estimate the maximum a-posteriori fold labelling assignment. The method achieved fold matching accuracy of 96.0% and 96.1% in patient cases with and without local colonic collapse. Moreover, it improved upon an existing surface-based registration algorithm by providing an initialisation. The set of landmark correspondences is used to non-rigidly transform a 2D source image derived from a conformal mapping process on the 3D endoluminal surface mesh. This achieves full surface correspondence between prone and supine views and can be further refined with an intensity based registration showing a statistically significant improvement (p<0.001p<0.001), and decreasing mean error from 11.9mm11.9mm to 6.0mm6.0mm measured at 1743 reference points from 17 CTC datasets

Impacts of conversion of tropical peat swamp forest to oil palm plantation on peat organic chemistry, physical properties and carbon stocks

Ecosystem services provided by tropical peat swamp forests, such as carbon (C) storage and water regulation, are under threat due to encroachment and replacement of these natural forests by drainage-based agriculture, commonly oil palm plantation. This study aims to quantify how the chemical and physical properties of peat change during land conversion to oil palm. This will be addressed by comparing four separate stages of conversion; namely, secondary peat swamp forests, recently deeply drained secondary forests, cleared and recently planted oil palm, and mature oil palm plantation in North Selangor, Malaysia. Results indicate accelerated peat decomposition in surface peats of mature oil palm plantations due to the lowered water table and altered litter inputs associated with this land-use change. Surface organic matter content and peat C stocks at secondary forest sites were higher than at mature oil palm sites (e.g. C stocks were 975 ± 151 and 497 ± 157 Mg ha− 1 at secondary forest and mature oil palm sites, respectively). Land conversion altered peat physical properties such as shear strength, bulk density and porosity, with mirrored changes above and below the water table. Our findings suggest close links between the organic matter and C content and peat physical properties through the entire depth of the peat profile. We have demonstrated that conversion from secondary peat swamp forest to mature oil palm plantation may seriously compromise C storage and, through its impact on peat physical properties, the water holding capacity in these peatlands

Color ptychography with a hyperspectral x-ray camera

A possible improvement on a new method of single acquisition hyperspectral (spectroscopic) ptychographic imaging, making use of a hyperspectral X-ray camera, is presented. Undulator tapering is used at the synchrotron to broaden the energy distribution of the X-ray beam to a suitable level for edge subtraction. The combination of a coherent imaging method such as ptychography with spectroscopy poses difficulties in experimental setup design regarding probe size. The final goal of the experiment, a K-edge subtraction, is not successful, but the technique is nevertheless promising. The capability of resolving the absorption edge applies to a wide range of research areas, such as element specific investigations in biological, materials, and earth sciences. We discuss the problems and their possible solutions

The effect of computer-aided detection markers on visual search and reader performance during concurrent reading of CT colonography

Objective: We aimed to identify the effect of computer-aided detection (CAD) on visual search and performance in CT Colonography (CTC) of inexperienced and experienced readers. Methods: Fifteen endoluminal CTC examinations were recorded, each with one polyp, and two videos were generated, one with and one without a CAD mark. Forty-two readers (17 experienced, 25 inexperienced) interpreted the videos during infrared visual search recording. CAD markers and polyps were treated as regions of interest in data processing. This multi-reader, multi-case study was analysed using multilevel modelling. Results: CAD drew readers’ attention to polyps faster, accelerating identification times: median ‘time to first pursuit’ was 0.48 s (IQR 0.27 to 0.87 s) with CAD, versus 0.58 s (IQR 0.35 to 1.06 s) without. For inexperienced readers, CAD also held visual attention for longer. All visual search metrics used to assess visual gaze behaviour demonstrated statistically significant differences when “with” and “without” CAD were compared. A significant increase in the number of correct polyp identifications across all readers was seen with CAD (74 % without CAD, 87 % with CAD; p < 0.001). Conclusions: CAD significantly alters visual search and polyp identification in readers viewing three-dimensional endoluminal CTC. For polyp and CAD marker pursuit times, CAD generally exerted a larger effect on inexperienced readers

Tracking eye gaze during interpretation of endoluminal three-dimensional CT colonography: visual perception of experienced and inexperienced readers

Purpose: To identify and compare key stages of the visual process in experienced and inexperienced readers and to examine how these processes are used to search a moving three-dimensional (3D) image and their relationship to false-negative errors. Materials and Methods: Institutional review board research ethics approval was granted to use anonymized computed tomographic (CT) colonographic data from previous studies and to obtain eye-tracking data from volunteers. Sixty-five radiologists (27 experienced, 38 inexperienced) interpreted 23 endoluminal 3D CT colonographic videos. Eye movements were recorded by using eye tracking with a desk-mounted tracker. Readers indicated when they saw a polyp by clicking a computer mouse. Polyp location and boundary on each video frame were quantified and gaze data were related to the polyp boundary for each individual reader and case. Predefined metrics were quantified and used to describe and compare visual search patterns between experienced and inexperienced readers by using multilevel modeling. Results: Time to first pursuit was significantly shorter in experienced readers (hazard ratio, 1.22 [95% confidence interval: 1.04, 1.44]; P = .017) but other metrics were not significantly different. Regardless of expertise, metrics such as assessment, identification period, and pursuit times were extended in videos where polyps were visible on screen for longer periods of time. In 97% (760 of 787) of observations, readers correctly pursued polyps. Conclusion: Experienced readers had shorter time to first eye pursuit, but many other characteristics of eye tracking were similar between experienced and inexperienced readers. Readers pursued polyps in 97% of observations, which indicated that errors during interpretation of 3D CT colonography in this study occurred in either the discovery or the recognition phase, but rarely in the scanning phase of radiologic image inspection