Gel phantom data for dynamic X-ray tomography

This is the documentation for dynamic X-ray tomography measurements of a gel phantom diffused with potassium iodide contrast agent. The measured data and additional materials are available at http://www.fips.fi/dataset.php and Zenodo (https://doi.org/10.5281/zenodo.3696817) for open use by the scientific community, as long as the data and this documentation at arXiv are appropriately referenced. The files contain: (1) 17 consecutive measurements of the gel phantom organized into sinograms at two different resolutions (binning levels) and some additional metadata which can be used to create matrix-free forward operators and filtered back-projection reconstructions; (2) the first measurement using a greater number of projections, and an additional measurement of an 18th time step using very dense angular sampling, for example to be used for reference reconstructions; (3) short example codes to showcase how the data could be used to test and validate reconstruction algorithms.Comment: Actual data can be found at https://doi.org/10.5281/zenodo.369681

Design and Construction of an X-ray Computed Tomography Imaging System

X-ray computed tomography (CT) is widely used in medical imaging and materials science. In this imaging modality, cross-sectional images of a physical object are formed by taking numerous X-ray projections from different angles and then applying a reconstruction algorithm to the measured data. The cross-sectional slices can be used to form a three-dimensional model of the interior structure of the object. CT is a prime example of an inverse problem, in which the aim is to recover an unknown cause from a known effect. CT technology continues to develop, motivated by the desire for increased image quality and spatial resolution in reconstructions. In medical CT, reducing patient dose is a major goal. The branch of CT known as X-ray microtomography (micro-CT) produces reconstructions with spatial resolutions in the micrometer range. Micro-CT has been practiced at the University of Helsinki since 2008. The research projects are often interdisciplinary, combining physics with fields such as biosciences, paleontology, geology, geophysics, metallurgy and food technology. This thesis documents the design and construction of a new X-ray imaging system for computed tomography. The system is a cone beam micro-CT scanner intended for teaching and research in inverse problems and X-ray physics. The scanner consists of a molybdenum target X-ray tube, a sample manipulator, and a flat panel detector, and it is built inside a radiation shielding cabinet. Measurements were made for calibrating the measurement geometry and for testing reconstruction quality. Two-dimensional reconstructions of various samples were computed using the plane which passes through the X-ray point source and is perpendicular to the axis of rotation. This central plane of the cone beam reduces to fan beam geometry. All reconstructions were computed using the filtered backprojection (FBP) algorithm, which is the industry standard. Tomographic reconstructions of high quality were obtained from the measurements. The results show that the imaging system is well suited for CT and the study of reconstruction algorithms.Tietokonetomografia (TT) on lääketieteellisessä kuvantamisessa ja materiaalitutkimuksessa laajalti käytetty menetelmä. Tämän kuvantamismuodon tavoitteena on muodostaa poikkileikkauskuvia fyysisestä kohteesta, mikä tapahtuu ottamalla röntgenprojektioita useista eri kulmista kohteen ympäriltä ja soveltamalla mittausdataan rekonstruktioalgoritmia. Poikkileikkauskuvista voidaan muodostaa kolmiulotteinen malli kohteen sisärakenteesta. Tietokonetomografia on malliesimerkki inversio-ongelmasta. Inversio-ongelmat ovat käänteisiä ongelmia, joissa pyritään määrittämään tunnetusta seurauksesta sen aiheuttanut tuntematon syy tai ilmiö. Tietokonetomografian yhä jatkuvan kehityksen taustalla on halu parantaa rekonstruktioiden paikkaerotuskykyä sekä kuvanlaatua. Lääketieteellisessä TT:ssä potilaan saaman annoksen pienentäminen on myös tärkeä tavoite. Röngtenmikrotomografia (mikro-TT) on tietokonetomografian osa-alue, jolla rekonstruktioissa saavutetaan mikrometriluokan paikkaerotuskyky. Helsingin yliopistolla mikro-TT:tä on käytetty tutkimusvälineenä vuodesta 2008 lähtien. Tutkimus muodostuu usein poikkitieteellisistä projekteista, joissa fysiikan menetelmiä käytetään tutkimaan esimerkiksi biotieteiden, paleontologian, geologian, geofysiikan, metallurgian ja ruokateknologian ongelmia. Tässä tutkielmassa esitellään tietokonetomografiaan tarkoitetun uuden röntgenkuvantamisjärjestelmän suunnittelu ja toteutus. Kuvantamisjärjestelmä on kartiokeilageometriaa käyttävä mikro-TT-skanneri, jota on tarkoitus käyttää inversio-ongelmien sekä röntgenfysiikan opetuksessa ja tutkimuksessa. Skanneri koostuu molybdeenikohtioisesta röntgenputkesta, näytteenpyörittimestä ja ilmaisimesta, jotka on sijoitettu säteilyltä suojaavaan mittaustilaan. Tämän työn mittaukset koostuivat kalibrointimittauksista, joilla pyrittiin määrittämään tarkasti laitteiston geometria, sekä rekonstruktioiden laadun tutkimista varten tehdyistä mittauksista. Eri näytteistä muodostettiin kaksiulotteisia poikkileikkauksia käyttäen kartiokeilasta sitä kuvaustasoa, joka kulkee röntgenputken pistelähteen läpi ja on kohtisuorassa näytteenpyörittimen pyörimisakseliin nähden. Tämä kartiokeilan keskitaso vastaa kaksiulotteista viuhkageometriaa. Kaikki rekonstruktiot laskettiin käyttämällä alan standardiksi muodostunutta suodatetun takaisinprojektion algoritmia (FBP-algoritmi). Mittauksista saatiin muodostettua korkeatasoisia tomografisia rekonstruktioita. Tulokset osoittavat, että rakennettu kuvantamisjärjestelmä soveltuu hyvin tietokonetomografiaan ja rekonstruktioalgoritmien tutkimiseen

JOINT RECONSTRUCTION IN LOW DOSE MULTI-ENERGY CT

Multi-energy CT takes advantage of the non-linearly varying attenuation properties of elemental media with respect to energy, enabling more precise material identification than single-energy CT. The increased precision comes with the cost of a higher radiation dose. A straightforward way to lower the dose is to reduce the number of projections per energy, but this makes tomographic reconstruction more ill-posed. In this paper, we propose how this problem can be overcome with a combination of a regularization method that promotes structural similarity between images at different energies and a suitably selected low-dose data acquisition protocol using non-overlapping projections. The performance of various joint regularization models is assessed with both simulated and experimental data, using the novel low-dose data acquisition protocol. Three of the models are well-established, namely the joint total variation, the linear parallel level sets and the spectral smoothness promoting regularization models. Furthermore, one new joint regularization model is introduced for multi-energy CT: a regularization based on the structure function from the structural similarity index. The findings show that joint regularization outperforms individual channel-by-channel reconstruction. Furthermore, the proposed combination of joint reconstruction and non-overlapping projection geometry enables significant reduction of radiation dose.Peer reviewe

Synergistic multi-spectral CT reconstruction with directional total variation

This work considers synergistic multi-spectral CT reconstruction where information from all available energy channels is combined to improve the reconstruction of each individual channel. We propose to fuse these available data (represented by a single sinogram) to obtain a polyenergetic image which keeps structural information shared by the energy channels with increased signal-to-noise ratio. This new image is used as prior information during a channel-by-channel minimization process through the directional total variation. We analyse the use of directional total variation within variational regularization and iterative regularization. Our numerical results on simulated and experimental data show improvements in terms of image quality and in computational speed. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.Peer reviewe

Automated daily quality control analysis for mammography in a multi-unit imaging center

Background: The high requirements for mammography image quality necessitate a systematic quality assurance process. Digital imaging allows automation of the image quality analysis, which can potentially improve repeatability and objectivity compared to a visual evaluation made by the users. Purpose: To develop an automatic image quality analysis software for daily mammography quality control in a multi-unit imaging center. Material and Methods: An automated image quality analysis software using the discrete wavelet transform and multi-resolution analysis was developed for the American College of Radiology accreditation phantom. The software was validated by analyzing 60 randomly selected phantom images from six mammography systems and 20 phantom images with different dose levels from one mammography system. The results were compared to a visual analysis made by four reviewers. Additionally, long-term image quality trends of a full-field digital mammography system and a computed radiography mammography system were investigated. Results: The automated software produced feature detection levels comparable to visual analysis. The agreement was good in the case of fibers, while the software detected somewhat more microcalcifications and characteristic masses. Long-term follow-up via a quality assurance web portal demonstrated the feasibility of using the software for monitoring the performance of mammography systems in a multi-unit imaging center. Conclusion: Automated image quality analysis enables monitoring the performance of digital mammography systems in an efficient, centralized manner.Peer reviewe

Promoter-Wide Hypermethylation of the Ribosomal RNA Gene Promoter in the Suicide Brain

BACKGROUND: Alterations in gene expression in the suicide brain have been reported and for several genes DNA methylation as an epigenetic regulator is thought to play a role. rRNA genes, that encode ribosomal RNA, are the backbone of the protein synthesis machinery and levels of rRNA gene promoter methylation determine rRNA transcription. METHODOLOGY/PRINCIPAL FINDINGS: We test here by sodium bisulfite mapping of the rRNA promoter and quantitative real-time PCR of rRNA expression the hypothesis that epigenetic differences in critical loci in the brain are involved in the pathophysiology of suicide. Suicide subjects in this study were selected for a history of early childhood neglect/abuse, which is associated with decreased hippocampal volume and cognitive impairments. rRNA was significantly hypermethylated throughout the promoter and 5' regulatory region in the brain of suicide subjects, consistent with reduced rRNA expression in the hippocampus. This difference in rRNA methylation was not evident in the cerebellum and occurred in the absence of genome-wide changes in methylation, as assessed by nearest neighbor. CONCLUSIONS/SIGNIFICANCE: This is the first study to show aberrant regulation of the protein synthesis machinery in the suicide brain. The data implicate the epigenetic modulation of rRNA in the pathophysiology of suicide

Over-use of thyroid testing in Canadian and UK primary care in frequent attenders : a cross-sectional study

Dr Greiver is supported through the Gordon F. Cheesbrough Research Chair in Family and Community Medicine from North York General Hospital.Background Thyroid stimulating hormone (TSH) is a common test used to detect and monitor clinically significant hypo- and hyperthyroidism. Population based screening of asymptomatic adults for thyroid disorders is not recommended. Objective The research objectives were to determine patterns of TSH testing in Canadian and English primary care practices, as well as patient and physician practice characteristics associated with testing TSH for primary care patients with no identifiable indication. Methods In this two-year cross-sectional observational study, Canadian and English electronic medical record databases were used to identify patients and physician practices. Cohorts of patients aged 18 years or older, without identifiable indications for TSH testing, were generated from these databases. Analyses were performed using a random-effects logistic regression to determine patient and physician practice characteristics associated with increased testing. We determined the proportion of TSH tests done concurrently with at least one common screening blood test (lipid profile or hemoglobin A1c). Standardized proportions of TSH test per family practice were used to examine the heterogeneity in the populations. Results At least one TSH test was done in 35.97 % (N=489,663) of Canadian patients and 29.36% (N=1,030,489) of English patients. Almost all TSH tests in Canada and England (95.69% and 99.23% respectively) were within the normal range (0.40-5.00 mU/L). A greater number of patient-physician encounters was the strongest predictor of TSH testing. 51.40% of TSH tests in Canada and 76.55% in England were done on the same day as at least one other screening blood test. There was no association between practice size and proportion of asymptomatic patients tested. Conclusions This comparative binational study found TSH patterns suggestive of over-testing and potentially thyroid disorder screening in both countries. There may be significant opportunities to improve appropriateness of TSH ordering in Canada and England and therefore improve allocation of limited system resources.PostprintPeer reviewe

Microwave Imaging for Neoadjuvant Chemotherapy Monitoring: Initial Clinical Experience

Introduction: Microwave tomography recovers images of tissue dielectric properties, which appear to be specific for breast cancer, with low-cost technology that does not present an exposure risk, suggesting the modality may be a good candidate for monitoring neoadjuvant chemotherapy. Methods: Eight patients undergoing neoadjuvant chemotherapy for locally advanced breast cancer were imaged longitudinally five to eight times during the course of treatment. At the start of therapy, regions of interest (ROIs) were identified from contrast-enhanced magnetic resonance imaging studies. During subsequent microwave examinations, subjects were positioned with their breasts pendant in a coupling fluid and surrounded by an immersed antenna array. Microwave property values were extracted from the ROIs through an automated procedure and statistical analyses were performed to assess short term (30 days) and longer term (four to six months) dielectric property changes. Results: Two patient cases (one complete and one partial response) are presented in detail and demonstrate changes in microwave properties commensurate with the degree of treatment response observed pathologically. Normalized mean conductivity in ROIs from patients with complete pathological responses was significantly different from that of partial responders (P value = 0.004). In addition, the normalized conductivity measure also correlated well with complete pathological response at 30 days (P value = 0.002). Conclusions: These preliminary findings suggest that both early and late conductivity property changes correlate well with overall treatment response to neoadjuvant therapy in locally advanced breast cancer. This result is consistent with earlier clinical outcomes that lesion conductivity is specific to differentiating breast cancer from benign lesions and normal tissue