Raw as Archival Still Image Format: A Consideration

Source materials like fine art, over-sized, fragile maps, and delicate artifacts have traditionally been digitally converted through the use of controlled lighting and high resolution scanners and camera backs. In addition the capture of items such as general and special collections bound monographs has recently grown both through consortial efforts like the Internet Archive's Open Content Alliance and locally at the individual institution level. These projects, in turn, have introduced increasingly higher resolution consumer-grade digital single lens reflex cameras or "DSLRs" as a significant part of the general cultural heritage digital conversion workflow. Central to the authors' discussion is the fact that both camera backs and DSLRs commonly share the ability to capture native raw file formats. Because these formats include such advantages as access to an image's raw mosaic sensor data within their architecture, many institutions choose raw for initial capture due to its high bit-level and unprocessed nature. However to date these same raw formats, so important to many at the point of capture, have yet to be considered "archival" within most published still imaging standards, if they are considered at all. Throughout many workflows raw files are deleted and thrown away after more traditionally "archival" uncompressed TIFF or JPEG 2000 files have been derived downstream from their raw source formats [1][2]. As a result, the authors examine the nature of raw anew and consider the basic questions, Should raw files be retained? What might their role be? Might they in fact form a new archival format space? Included in the discussion is a survey of assorted raw file types and their attributes. Also addressed are various sustainability issues as they pertain to archival formats with a special emphasis on both raw's positive and negative characteristics as they apply to archival practices. Current common archival workflows versus possible raw-based ones are investigated as well. These comparisons are noted in the context of each approach's differing levels of usable captured image data, various preservation virtues, and the divergent ideas of strictly fixed renditions versus the potential for improved renditions over time. Special attention is given to the DNG raw format through a detailed inspection of a number of its various structural components and the roles that they play in the format's latest specification. Finally an evaluation is drawn of both proprietary raw formats in general and DNG in particular as possible alternative archival formats for still imaging.

An image-based method to automatically propagate bony landmarks: application to computational spine biomechanics.

In attempts to elucidate the underlying mechanisms of spinal injuries and spinal deformities, several experimental and numerical studies have been conducted to understand the biomechanical behavior of the spine. However, numerical biomechanical studies suffer from uncertainties associated with hard- and soft-tissue anatomies. Currently, these parameters are identified manually on each mesh model prior to simulations. The determination of soft connective tissues on finite element meshes can be a tedious procedure, which limits the number of models used in the numerical studies to a few instances. In order to address these limitations, an image-based method for automatic morphing of soft connective tissues has been proposed. Results showed that the proposed method is capable to accurately determine the spatial locations of predetermined bony landmarks. The present method can be used to automatically generate patient-specific models, which may be helpful in designing studies involving a large number of instances and to understand the mechanical behavior of biomechanical structures across a given population.

Image-based vs. mesh-based statistical appearance models of the human femur: Implications for finite element simulations.

Statistical appearance models have recently been introduced in bone mechanics to investigate bone geometry and mechanical properties in population studies. The establishment of accurate anatomical correspondences is a critical aspect for the construction of reliable models. Depending on the representation of a bone as an image or a mesh, correspondences are detected using image registration or mesh morphing. The objective of this study was to compare image-based and mesh-based statistical appearance models of the femur for finite element (FE) simulations. To this aim, (i) we compared correspondence detection methods on bone surface and in bone volume; (ii) we created an image-based and a mesh-based statistical appearance models from 130 images, which we validated using compactness, representation and generalization, and we analyzed the FE results on 50 recreated bones vs. original bones; (iii) we created 1000 new instances, and we compared the quality of the FE meshes. Results showed that the image-based approach was more accurate in volume correspondence detection and quality of FE meshes, whereas the mesh-based approach was more accurate for surface correspondence detection and model compactness. Based on our results, we recommend the use of image-based statistical appearance models for FE simulations of the femur.

Image-based biomechanical assessment of vertebral body and intervertebral disc in the human lumbar spine

Life expectancy continuously increases but our society faces age-related conditions. Among musculoskeletal diseases, osteoporosis associated with risk of vertebral fracture and degenerative intervertebral disc (IVD) are painful pathologies responsible for tremendous healthcare costs. Hence, reliable diagnostic tools are necessary to plan a treatment or follow up its efficacy. Yet, radiographic and MRI techniques, respectively clinical standards for evaluation of bone strength and IVD degeneration, are unspecific and not objective. Increasingly used in biomedical engineering, CT-based finite element (FE) models constitute the state-of-art for vertebral strength prediction. However, as non-invasive biomechanical evaluation and personalised FE models of the IVD are not available, rigid boundary conditions (BCs) are applied on the FE models to avoid uncertainties of disc degeneration that might bias the predictions. Moreover, considering the impact of low back pain, the biomechanical status of the IVD is needed as a criterion for early disc degeneration. Thus, the first FE study focuses on two rigid BCs applied on the vertebral bodies during compression test of cadaver vertebral bodies, vertebral sections and PMMA embedding. The second FE study highlights the large influence of the intervertebral disc’s compliance on the vertebral strength, damage distribution and its initiation. The third study introduces a new protocol for normalisation of the IVD stiffness in compression, torsion and bending using MRI-based data to account for its morphology. In the last study, a new criterion (Otsu threshold) for disc degeneration based on quantitative MRI data (axial T2 map) is proposed. The results show that vertebral strength and damage distribution computed with rigid BCs are identical. Yet, large discrepancies in strength and damage localisation were observed when the vertebral bodies were loaded via IVDs. The normalisation protocol attenuated the effect of geometry on the IVD stiffnesses without complete suppression. Finally, the Otsu threshold computed in the posterior part of annulus fibrosus was related to the disc biomechanics and meet objectivity and simplicity required for a clinical application. In conclusion, the stiffness normalisation protocol necessary for consistent IVD comparisons and the relation found between degeneration, mechanical response of the IVD and Otsu threshold lead the way for non-invasive evaluation biomechanical status of the IVD. As the FE prediction of vertebral strength is largely influenced by the IVD conditions, this data could also improve the future FE models of osteoporotic vertebra.

Graphical Model-Based Vertebra Identification from X-Ray Image(s)

Automated identification of vertebrae from X-ray image(s) is an important step for various medical image computing tasks such as 2D/3D rigid and non-rigid registration. In this chapter we present a graphical model-based solution for automated vertebra identification from X-ray image(s). Our solution does not ask for a training process using training data and has the capability to automatically determine the number of vertebrae visible in the image(s). This is achieved by combining a graphical model-based maximum a posterior probability (MAP) estimate with a mean-shift based clustering. Experiments conducted on simulated X-ray images as well as on a low-dose low quality X-ray spinal image of a scoliotic patient verified its performance.

Ruler Based Automatic C-Arm Image Stitching Without Overlapping Constraint

In this paper, we propose a new method for stitching multiple fluoroscopic images taken by a C-arm instrument. We employ an X-ray radiolucent ruler with numbered graduations while acquiring the images, and the image stitching is based on detecting and matching ruler parts in the images to the corresponding parts of a virtual ruler. To achieve this goal, we first detect the regular spaced graduations on the ruler and the numbers. After graduation labeling, for each image, we have the location and the associated number for every graduation on the ruler. Then, we initialize the panoramic X-ray image with the virtual ruler, and we “paste” each image by aligning the detected ruler part on the original image, to the corresponding part of the virtual ruler on the panoramic image. Our method is based on ruler matching but without the requirement of matching similar feature points in pairwise images, and thus, we do not necessarily require overlap between the images. We tested our method on eight different datasets of X-ray images, including long bones and a complete spine. Qualitative and quantitative experiments show that our method achieves good results.

XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry

XMapTools is a MATLAB©-based graphical user interface program for electron microprobe X-ray image processing, which can be used to estimate the pressure–temperature conditions of crystallization of minerals in metamorphic rocks. This program (available online at http://www.xmaptools.com) provides a method to standardize raw electron microprobe data and includes functions to calculate the oxide weight percent compositions for various minerals. A set of external functions is provided to calculate structural formulae from the standardized analyses as well as to estimate pressure–temperature conditions of crystallization, using empirical and semi-empirical thermobarometers from the literature. Two graphical user interface modules, Chem2D and Triplot3D, are used to plot mineral compositions into binary and ternary diagrams. As an example, the software is used to study a high-pressure Himalayan eclogite sample from the Stak massif in Pakistan. The high-pressure paragenesis consisting of omphacite and garnet has been retrogressed to a symplectitic assemblage of amphibole, plagioclase and clinopyroxene. Mineral compositions corresponding to ~165,000 analyses yield estimates for the eclogitic pressure–temperature retrograde path from 25 kbar to 9 kbar. Corresponding pressure–temperature maps were plotted and used to interpret the link between the equilibrium conditions of crystallization and the symplectitic microstructures. This example illustrates the usefulness of XMapTools for studying variations of the chemical composition of minerals and for retrieving information on metamorphic conditions on a microscale, towards computation of continuous pressure–temperature-and relative time path in zoned metamorphic minerals not affected by post-crystallization diffusion.

Improving 4D plan quality for PBS-based liver tumour treatments by combining online image guided beam gating with rescanning.

Pencil beam scanned (PBS) proton therapy has many advantages over conventional radiotherapy, but its effectiveness for treating mobile tumours remains questionable. Gating dose delivery to the breathing pattern is a well-developed method in conventional radiotherapy for mitigating tumour-motion, but its clinical efficiency for PBS proton therapy is not yet well documented. In this study, the dosimetric benefits and the treatment efficiency of beam gating for PBS proton therapy has been comprehensively evaluated. A series of dedicated 4D dose calculations (4DDC) have been performed on 9 different 4DCT(MRI) liver data sets, which give realistic 4DCT extracting motion information from 4DMRI. The value of 4DCT(MRI) is its capability of providing not only patient geometries and deformable breathing characteristics, but also includes variations in the breathing patterns between breathing cycles. In order to monitor target motion and derive a gating signal, we simulate time-resolved beams' eye view (BEV) x-ray images as an online motion surrogate. 4DDCs have been performed using three amplitude-based gating window sizes (10/5/3 mm) with motion surrogates derived from either pre-implanted fiducial markers or the diaphragm. In addition, gating has also been simulated in combination with up to 19 times rescanning using either volumetric or layered approaches. The quality of the resulting 4DDC plans has been quantified in terms of the plan homogeneity index (HI), total treatment time and duty cycle. Results show that neither beam gating nor rescanning alone can fully retrieve the plan homogeneity of the static reference plan. Especially for variable breathing patterns, reductions of the effective duty cycle to as low as 10% have been observed with the smallest gating rescanning window (3 mm), implying that gating on its own for such cases would result in much longer treatment times. In addition, when rescanning is applied on its own, large differences between volumetric and layered rescanning have been observed as a function of increasing number of re-scans. However, once gating and rescanning is combined, HI to within 2% of the static plan could be achieved in the clinical target volume, with only moderately prolonged treatment times, irrespective of the rescanning strategy used. Moreover, these results are independent of the motion surrogate used. In conclusion, our results suggest image guided beam gating, combined with rescanning, is a feasible, effective and efficient motion mitigation approach for PBS-based liver tumour treatments.

A Novel Ultrasound-Based Registration for Image-Guided Laparoscopic Liver Ablation.

BACKGROUND Patient-to-image registration is a core process of image-guided surgery (IGS) systems. We present a novel registration approach for application in laparoscopic liver surgery, which reconstructs in real time an intraoperative volume of the underlying intrahepatic vessels through an ultrasound (US) sweep process. METHODS An existing IGS system for an open liver procedure was adapted, with suitable instrument tracking for laparoscopic equipment. Registration accuracy was evaluated on a realistic phantom by computing the target registration error (TRE) for 5 intrahepatic tumors. The registration work flow was evaluated by computing the time required for performing the registration. Additionally, a scheme for intraoperative accuracy assessment by visual overlay of the US image with preoperative image data was evaluated. RESULTS The proposed registration method achieved an average TRE of 7.2 mm in the left lobe and 9.7 mm in the right lobe. The average time required for performing the registration was 12 minutes. A positive correlation was found between the intraoperative accuracy assessment and the obtained TREs. CONCLUSIONS The registration accuracy of the proposed method is adequate for laparoscopic intrahepatic tumor targeting. The presented approach is feasible and fast and may, therefore, not be disruptive to the current surgical work flow.

Design and Optimization of Four-dimensional Cone-beam Computed Tomography in Image-guided Radiation Therapy

The influence of respiratory motion on patient anatomy poses a challenge to accurate radiation therapy, especially in lung cancer treatment. Modern radiation therapy planning uses models of tumor respiratory motion to account for target motion in targeting. The tumor motion model can be verified on a per-treatment session basis with four-dimensional cone-beam computed tomography (4D-CBCT), which acquires an image set of the dynamic target throughout the respiratory cycle during the therapy session. 4D-CBCT is undersampled if the scan time is too short. However, short scan time is desirable in clinical practice to reduce patient setup time. This dissertation presents the design and optimization of 4D-CBCT to reduce the impact of undersampling artifacts with short scan times. This work measures the impact of undersampling artifacts on the accuracy of target motion measurement under different sampling conditions and for various object sizes and motions. The results provide a minimum scan time such that the target tracking error is less than a specified tolerance. This work also presents new image reconstruction algorithms for reducing undersampling artifacts in undersampled datasets by taking advantage of the assumption that the relevant motion of interest is contained within a volume-of-interest (VOI). It is shown that the VOI-based reconstruction provides more accurate image intensity than standard reconstruction. The VOI-based reconstruction produced 43% fewer least-squares error inside the VOI and 84% fewer error throughout the image in a study designed to simulate target motion. The VOI-based reconstruction approach can reduce acquisition time and improve image quality in 4D-CBCT.

Examining the Relationship Between Media Use and Aggression, Sexuality, and Body Image

Objectives: The primary purpose of this research is to understand the media's impact on individual attitudes and behaviors related to aggression, sexuality, and body image. This research is of particular importance because it uses up-to-date data reflecting effects based on the current media environment. Additionally, it includes a racially diverse sample. Methods: A survey of 407 students at a large, public university was conducted. The survey instrument contained general measures related to media consumption, including overall television, video game, and internet use, as well as more specific questions related to particular types of media, such as pornography. For the dependent variables, questions were included that measured both attitudes and behaviors related to aggression, sexuality, and body image. Results: Consistent with predictions, media use impacted both attitudes and behaviors related to aggression, sexuality, and body image. Specifically, overall television consumption led to increased levels of aggression (r=.18, pr=.20, pr=.24, pr=.42, pr=.40, p Conclusions: The media continue to play an important role in the development of attitudes and behaviors. It is warranted, therefore, to continue to investigate what media can cause negative outcomes, as well as to determine how those outcomes vary based on race and gender.

Design, Synthesis and Development of Transporter Targeting Agents for Image-guided Therapy and Drug Delivery

The purpose of this study was to design, synthesize and develop novel transporter targeting agents for image-guided therapy and drug delivery. Two novel agents, N4-guanine (N4amG) and glycopeptide (GP) were synthesized for tumor cell proliferation assessment and cancer theranostic platform, respectively. N4amG and GP were synthesized and radiolabeled with 99mTc and 68Ga. The chemical and radiochemical purities as well as radiochemical stabilities of radiolabeled N4amG and GP were tested. In vitro stability assessment showed both 99mTc-N4amG and 99mTc-GP were stable up to 6 hours, whereas 68Ga-GP was stable up to 2 hours. Cell culture studies confirmed radiolabeled N4amG and GP could penetrate the cell membrane through nucleoside transporters and amino acid transporters, respectively. Up to 40% of intracellular 99mTc-N4amG and 99mTc-GP was found within cell nucleus following 2 hours of incubation. Flow cytometry analysis revealed 99mTc-N4amG was a cell cycle S phase-specific agent. There was a significant difference of the uptake of 99mTc-GP between pre- and post- paclitaxel-treated cells, which suggests that 99mTc-GP may be useful in chemotherapy treatment monitoring. Moreover, radiolabeled N4amG and GP were tested in vivo using tumor-bearing animal models. 99mTc-N4amG showed an increase in tumor-to-muscle count density ratios up to 5 at 4 hour imaging. Both 99mTc-labeled agents showed decreased tumor uptake after paclitaxel treatment. Immunohistochemistry analysis demonstrated that the uptake of 99mTc-N4amG was correlated with Ki-67 expression. Both 99mTc-N4amG and 99mTc-GP could differentiate between tumor and inflammation in animal studies. Furthermore, 68Ga-GP was compared to 18F-FDG in rabbit PET imaging studies. 68Ga-GP had lower tumor standardized uptake values (SUV), but similar uptake dynamics, and different biodistribution compared with 18F-FDG. Finally, to demonstrate that GP can be a potential drug carrier for cancer theranostics, several drugs, including doxorubicin, were selected to be conjugated to GP. Imaging studies demonstrated that tumor uptake of GP-drug conjugates was increased as a function of time. GP-doxorubicin (GP-DOX) showed a slow-release pattern in in vitro cytotoxicity assay and exhibited anti-cancer efficacy with reduced toxicity in in vivo tumor growth delay study. In conclusion, both N4amG and GP are transporter-based targeting agents. Radiolabeled N4amG can be used for tumor cell proliferation assessment. GP is a potential agent for image-guided therapy and drug delivery.