Computer assisted detection of abnormal airway variation in CT scans related to paediatric tuberculosis.

Airway deformation and stenosis can be key signs of pathology such as lymphadenopathy. This study presents a local airway point distribution model (LA-PDM) to automatically analyse regions of the airway tree in CT scans and identify abnormal airway deformation. In our method, the airway tree is segmented and the centreline identified from each chest CT scan. Thin-plate splines, along with a local mesh alignment method for tubular meshes, are used to register the airways and develop point distribution models (PDM). Each PDM is then used to analyse and classify local regions of the airway. This LA-PDM method was developed using 89 training cases and evaluated on a 90 CT test set, where each set includes paediatric tuberculosis (TB) cases (with airway involvement) and non-TB cases (without airway involvement). The LA-PDM was able to accurately distinguish cases with airway involvement with an AUC of the ROC classification (and 95% confidence interval) of 0.87 (0.77-0.94) for the Trachea-LMB-RMB region and 0.81 (0.68-0.90) for the RMB-RUL-BI region - outperforming a comparison method based on airway cross-sectional features. This has the potential to assist and improve airway analysis from CT scans by detecting involved airways and visualising affected airway regions.

An in vivo subject-specific 3D functional knee joint model using combined MR imaging.

PURPOSE: We aim to quantitatively characterise the knee joint function in vivo under body-weight-bearing conditions via subject-specific models extracted from magnetic resonance (MR) data, in order to better understand the knee joint kinematic function in 3D. METHODS: Six healthy volunteers without any record of knee abnormality were scanned using a combined MR imaging strategy to record quasi-squatting motion and 3D knee anatomy. After a semi-automatic segmentation to delineate tibio-femoral articulation components, motion data were mapped to the anatomical data using a bi-rigid registration in order to achieve six degrees of freedom. The individual knee joint function was characterised by analysing the tibio-femoral articulation contact mechanism based on the reconstructed models in 3D and MR images in 2D. Contact points were extracted and their trajectory was plotted on the tibia plateau. RESULTS: The 3D models clearly show the relative rotation and gliding between tibia and femur during global flexion. Within the measured flexion arc, the contact points move less between 30[Formula: see text] and 100[Formula: see text] on both tibial plateaux as compared to that on the rest of the flexion arc. Four out of the six volunteers showed a global pattern of less moving extent of contact points on the medial tibial plateau than on the lateral tibial plateau in both 3D and 2D. CONCLUSION: The proposed subject-specific model is able to characterise knee joint kinematic function. It provides a way to describe knee joint surface kinematics quantitatively, which may help to better understand the knee function and joint derangements.

Identification of paediatric tuberculosis from airway shape features.

Clinical signs of paediatric pulmonary tuberculosis (TB) include stenosis and deformation of the airways. This paper presents two methods to analyse airway shape and detect airway pathology from CT images. Features were extracted using (1) the principal components of the airway surface mesh and (2) branch radius and orientation features. These methods were applied to a dataset of 61 TB and non-TB paediatric patients. Nested cross-validation of the support vector classifier found the sensitivity of detecting TB to be 86% and a specificity of 91% for the first 10 PCA modes while radius based features had a sensitivity of 86% and a specificity of 94%. These methods show the potential of computer assisted detection of TB and other airway pathology from airway shape deformation.

2D/3D fetal cardiac dataset segmentation using a deformable model.

PURPOSE: To segment the fetal heart in order to facilitate the 3D assessment of the cardiac function and structure. METHODS: Ultrasound acquisition typically results in drop-out artifacts of the chamber walls. The authors outline a level set deformable model to automatically delineate the small fetal cardiac chambers. The level set is penalized from growing into an adjacent cardiac compartment using a novel collision detection term. The region based model allows simultaneous segmentation of all four cardiac chambers from a user defined seed point placed in each chamber. RESULTS: The segmented boundaries are automatically penalized from intersecting at walls with signal dropout. Root mean square errors of the perpendicular distances between the algorithm's delineation and manual tracings are within 2 mm which is less than 10% of the length of a typical fetal heart. The ejection fractions were determined from the 3D datasets. We validate the algorithm using a physical phantom and obtain volumes that are comparable to those from physically determined means. The algorithm segments volumes with an error of within 13% as determined using a physical phantom. CONCLUSIONS: Our original work in fetal cardiac segmentation compares automatic and manual tracings to a physical phantom and also measures inter observer variation.

Texture-based quantification of lumbar intervertebral disc degeneration from conventional T2-weighted MRI.

BACKGROUND: Disc degeneration quantification is important for monitoring the effects of new therapeutic methods, such as cell and growth factor therapy. Magnetic resonance (MR) image texture reflects biochemical and structural tissue properties and has been used for differentiating between normal and pathological status in a variety of medical applications. PURPOSE: To investigate the suitability of textural descriptors for the quantification of intervertebral disc degeneration using conventional T2-weighted magnetic resonance images of the lumbar spine. MATERIAL AND METHODS: A 3 Tesla scanner was used, and conventional T2- weighted MR images were obtained, and a total of 255 lumbar discs were analyzed. An atlas-based method was used for segmenting the disc regions from the images. A set of first and second order statistics describing texture of each region were calculated. The validity and reliability of these descriptors for disc degeneration severity quantification was tested through their correlation with patient age and qualitative clinical grading of degeneration severity. Texture quantification results were compared to a widely accepted method for disc degeneration quantification based on the measurement of disc's mean signal intensity. RESULTS: Out of the set of texture descriptors tested, two descriptors quantifying image intensity inhomogeneity, i.e. the grey level standard deviation and co-occurrence derived sum of squares displayed the strongest association to patient age and clinical grading of disc degeneration severity (P<0.001). This is attributed to these inhomogeneity descriptors' capability to capture the progressive loss of nucleus-annulus distinction in the degenerative progress. Statistical analysis indicates that these descriptors can effectively separate between early stages of degeneration. Quantitative measurements are highly repeatable (intraclass correlation >0.98). CONCLUSION: Inhomogeneity descriptors could be a valuable tool for tracking the evolution of disc degeneration and monitoring the response to treatment in a simple, precise and repeatable manner.

Comparison of pencil beam and collapsed cone algorithms, in radiotherapy treatment planning for 6 and 10 MV photon.

BACKGROUND: In radiotherapy treatment, the calculation of radiation dose distribution in target volume lead to an optimum set of planning parameters. This worked has been aimed to compare two photon beam dose calculation algorithms in the Oncentra Treatment Planning system for Varian Linear Accelerator, to assure the quality of treatment planning. METHODS: Monitor Units to be delivered on normalization depth in patient has been calculated using the pencil beam and collapsed cone algorithms for two photon energies 6 and 10 MV. The percentage depth dose and beam profiles for 21 treatment fields, for both the calculation systems have been compared for both photon energies. RESULTS: The percentage depth doses and beam profiles for both calculation systems are comparable in large field sizes as well as central axis field settings. The doses normalization depth deviate for some field settings, but in central axis large field sizes the difference within tolerance limits. CONCLUSION: Both calculation algorithms are in close agreement in most of the field settings (mainly in central axis fields), within tolerance level. The difference is relatively greater in small field sizes and off-axis field settings.

Atlas-based segmentation of degenerated lumbar intervertebral discs from MR images of the spine.

Intervertebral disc degeneration is an age-associated condition related to chronic back pain, while its consequences are responsible for over 90 % of spine surgical procedures. In clinical practice, MRI is the modality of reference for diagnosing disc degeneration. In this study, we worked toward 2-D semiautomatic segmentation of both normal and degenerated lumbar intervertebral discs from T2-weighted midsagittal MR images of the spine. This task is challenged by partial volume effects and overlapping gray-level values between neighboring tissue classes. To overcome these problems three variations of atlas-based segmentation using a probabilistic atlas of the intervertebral disc were developed and their accuracies were quantitatively evaluated against manually segmented data. The best overall performance, when considering the tradeoff between segmentation accuracy and time efficiency, was accomplished by the atlas-robust-fuzzy c-means approach, which combines prior anatomical knowledge by means of a rigidly registered probabilistic disc atlas with fuzzy clustering techniques incorporating smoothness constraints. The dice similarity indexes of this method were 91.6 % for normal and 87.2 % for degenerated discs. Research in progress utilizes the proposed approach as part of a computer-aided diagnosis system for quantification and characterization of disc degeneration severity. Moreover, this approach could be exploited in computer-assisted spine surgery.

Feasibility of dynamic 3-D color Doppler ultrasound for imaging penile vascular change in renal transplant patients with erectile dysfunction responding to sildenafil.

Renal transplant recipients (RTRs) have a high incidence of erectile dysfunction (ED). Differentiation of penile vasculogenic impotence from other causes is important for treatment. Conventional 2-D color Doppler assessment after intracavernosal stimulant injection often fails to produce reliable results because of limited views by the cross-sectional imaging and the painful procedure. In comparison to the findings in three healthy volunteers, we determined cavernosal vascular hemodynamics in eight RTRs with ED before and after oral sildenafil by using live 3-D ultrasound and dynamic 3-D color Doppler. Results showed that, before sildenafil, penile arterial flow signals could only be reliably detected in one patient. After sildenafil, all had reliably detectable flow with grades II to III erection. Our data suggest that 3-D volumetric changes of the penis and its vasculature during erection can be studied by this technique and that this method could be useful for the evaluation of new drugs and therapeutic biofeedback.

Minimally-compressive, three- and four-dimensional ultrasound imaging of the clitoris: a feasibility study.

There has been no objective means for imaging the three-dimensional (3D) morphology of the clitoris-a poorly understood, complex structure. A Live 3D ultrasound system with a matrix-array transducer was used for data acquisition from eight women. The transducer was positioned in front of and about 3 cm away from the clitoris, with a gel pad or water pad being placed in between. The pads allowed the delicate structures to be imaged without noticeable deformation. Quality images could be obtained with use of a water pad in all patients. The imaging volume was big enough to cover the clitoral glans and body simultaneously, allowing real-time 3D visualisation. To cover the entire clitoris, the probe was moved from one side of the crus to the other, or a four subvolume scan was performed. 3D clitoral anatomy was depicted from 71% of 51 water pad data-sets. The study demonstrates the feasibility of obtaining 3D clitoral ultrasound images. This will improve scientific and clinical understanding of the clitoral role in sexual activity. The minimally-compressive scanning offers an opportunity to visualise dynamic 3D (4D) morphology of other deformable body parts.

Analysis of CD36 expression on human monocytic cells and atherosclerotic tissue sections with quantum dots: investigation by flow cytometry and spectral imaging microscopy.

OBJECTIVE: To demonstrate CD36 expression with quantum dots (QDs) 525 and/or 605 on human monocytic U937 cells and atherosclerotic tissue sections by means of flow cytometry (FCM) and/or confocal laser scanning microscopy (CLSM). STUDY DESIGN: U937 cells and tissue sections were analyzed by means of FCM and/or CLSM. FCM was performed, using different ultraviolet (UV) and visible (488/532 nm) excitation modes. In the visible mode, fluorescence intensities of QDs, phycoerythrin (PE) and fluorescein isothiocyanate (FITC) were compared. Three-dimensional (3-D) sequences of images were obtained by spectral analysis in a CLSM and analyzed by the factor analysis of medical image sequences (FAMIS) algorithm, providing factor curves and images. Factor images are the result of the FAMIS image processing method, which differentiates emission spectra from 3D sequences of images. In CLSM analysis, preparations are screened in a UV excitation mode to optimize the possibilities of QDs and have the benefit of 4',6-diamino-2-phenylindole or Hoechst 33342 counterstaining of nuclei. RESULTS: FCM and CLSM revealed CD36 expression by means of QDs 525 and/or 605. Fluorescence intensity of PE and of FITC was higher than that of QDs 525 and of 605. As factor curves and images show the red emission of QDs 605 only, subsequent reliable identification and localization of CD36 was obtained. CONCLUSION: QDs 525 and 605 are useful to analyze antigenic expression. Following FCM, which is well adapted to detect fluorescence emission of QDs in the UV or visible excitation mode, CLSM and subsequent spectral analysis assess more specific characterization of QD fluorescent emissions.

Real-time three-dimensional ultrasound visualization of erection and artificial coitus.

To investigate the feasibility of imaging penile erection and coitus in real time and in three dimensions, a 'Live' three-dimensional (3-D) ultrasound system was used to acquire the volume of interest at 25 Hz from five healthy men. Water baths and gel-made artificial vaginas were devised to facilitate the 3-D scans without the probe being in direct contact with the penis. For the first volunteer scanned with the water bath alone, the penis failed to erect within 30 min. For the other four volunteers, the 'vagina' successfully initiated and maintained the erection and allowed artificial intercourse. Results have shown that the 'Live' 3-D ultrasound and minimally compressive imaging techniques together can offer an objective means for visualizing erection and coitus in spatial totality and temporal reality. They can be further developed to reveal more reliable details about the dynamic morphology, improving scientific understanding of sexual activities and clinical management of related problems.

7-Ketocholesterol favors lipid accumulation and colocalizes with Nile Red positive cytoplasmic structures formed during 7-ketocholesterol-induced apoptosis: analysis by flow cytometry, FRET biphoton spectral imaging microscopy, and subcellular fractionation.

BACKGROUND: Oxidized low-density lipoproteins play key roles in atherosclerosis. Their toxicity is at least in part due to 7-ketocholesterol (7KC), which is a potent inducer of apoptosis. In this study on human promonocytic U937 cells, we determined the effects and the interactions of 7KC with cellular lipids during 7KC-induced apoptosis. METHODS: Morphologic and functional changes were investigated by microscopic and flow cytometric methods after staining with propidium iodide, 3,3'-dihexyloxacarbocyanine iodide, and Hoechst 33342. Cellular lipid content was identified by using filipin to quantify free cholesterol and Nile Red (NR), which emit a yellow or orange-red fluorescence in the presence of neutral and polar lipids, respectively. After staining with NR, interactions of 7KC with cellular lipids were identified by fluorescence resonance energy transfer biphoton spectral imaging confocal microscopy and by subcellular fractionation, gas chromatography, and mass spectrometry. RESULTS: During 7KC-induced apoptosis the fluorescence from filipin and the ratio of measured (orange-red vs. yellow) fluorescence of NR were enhanced. Spectral analysis of images obtained in biphoton mode and resulting factor images demonstrated the occurrence of fluorescence resonance energy transfer between 7KC and NR and the subsequent colocalization of 7KC and NR. These data were in agreement with biochemical characterization and demonstrated that 7KC and neutral and polar lipids accumulate in NR-stained cytoplasmic structures. CONCLUSIONS: During 7KC-induced apoptosis, 7KC modifies the cellular content of neutral and polar lipids, favors free cholesterol accumulation, and colocalizes with neutral and polar lipids that are inside NR-stained cytoplasmic structures.

Analysis of fluorescent MRI contrast agent behavior in the liver and thoracic aorta of mice.

OBJECTIVE: To characterize the behavior of magnetofluorescent products injected in mice intravenously. STUDY DESIGN: The magnetic resonance imaging (MRI) products were labelled with fluorescent molecules to examine the biodistribution process in vivo and observe them at the cellular level by means of confocal microscopy. Three-dimensional (3D) sequences of images were obtained by spectral analysis of sample preparations in a multiphoton confocal microscope and analyzed by the factor analysis of medical image sequence algorithm, which provides factor curves. Factor images are the result of image-processing methods that utilize information from emission spectra. Preparations are also screened in the counting mode to provide fluorescent lifetime imaging microscopy (FLIM) characterizations. RESULTS: Factor images and FLIM images can help to analyze MRI targeting inside the liver and thoracic aorta of mice. They show positive detection of Fe-Texas red and BOPTA-Eu in the liver and positive detection of Fe-Texas red and negative detection of BOPTA-Eu inside the thoracic aorta. CONCLUSION: This investigation established the utility of fluorescent MRI contrast agents as in vivo staining tools for cellular sites.

Multiple excitation confocal analysis of targets in nuclei of cytogenetic preparations.

OBJECTIVE: To demonstrate that cellular preparations requiring color analysis of different domains stained by molecular cytogenetic methods (fluorescence in situ hybridization) can be processed by spectral analysis of fluorescent emissions by either factor analysis of medical image sequences (FAMIS) or a META confocal configuration to isolate fluorescent probes. STUDY DESIGN: Three-dimensional sequences of images obtained by spectral analysis in a META confocal microscope (Carl Zeiss SAS, Jena, Germany) were analyzed by META processing and the FAMIS algorithm, which provides factor curves. META and factor images were then the result of image-processing methods that cover emission spectra. RESULTS: Factor curves and factor or META images can help to analyze targets inside nuclei. CONCLUSION: It is possible to process preparations containing numerous spots on different colors to differentiate stained targets and to improve visualization and detection.

Analysis of the fluorescence of monodansylcadaverine-positive cytoplasmic structures during 7-ketocholesterol-induced cell death.

OBJECTIVE: To analyze multilamellar cytoplasmic structures by confocal laser scanning microscopy (CLSM) combined with factor analysis of biomedical image sequences (FAMIS). STUDY DESIGN: After treatment of U937 cells with 7-ketocholesterol (7-keto), cytoplasmic alterations were assessed with monodansylcadaverine (MDC). By ultraviolet excitation of a confocal laser scanning microscope (UV-CLSM), spectral sequences were performed to characterize 7-keto and MDC distribution inside cells. FAMIS was used to transform the image sequences in factor curves and images. RESULTS: By UV-CLSM, 7-keto fluorescence was detected together with MDC, which revealed morphologic cytoplasmic changes in cells. The factor images obtained from confocal image sequences emphasized the view of these results. These data are in agreement with biochemical characterizations of MDC-positive structures. CONCLUSION: The combined use of confocal microscopy and FAMIS allowed us to detect MDC-positive cytoplasmic structures in 7-keto-treated cells and to colocalize MDC and 7-keto distribution. This new method confirms the usefulness of MDC as a marker of oxysterol-induced cell death.

FRET multiphoton spectral imaging microscopy of 7-ketocholesterol and Nile Red in U937 monocytic cells loaded with 7-ketocholesterol.

OBJECTIVE: To show the effect of 7-ketocholesterol (7KC) on cellular lipid content by means of flow cytometry and the interaction of 7KC with Nile Red (NR) via ultraviolet fluorescence resonance energy transfer (FRET) excitation of NR on U937 monocytic cells by means of 2-photon excitation confocal laser scanning microscopy (CLSM). STUDY DESIGN: Untreated and 7KC-treated U937 cells were stained with NR and analyzed by flow cytometry and CLSM. 3D sequences of images were obtained by spectral analysis in a 2-photon excitation CLSM and analyzed by the factor analysis of medical image sequences (FAMIS) algorithm, which provides factor curves and images. Factor images are the result of the FAMIS image processing method, which handles emission spectra. In FRET analysis, preparations are screened at selected UV wavelengths to avoid emission of NR in the absence of 7KC. RESULTS: During 7KC-induced cell death,flow cytometry and CLSM revealed a modification of the cellular lipid content. Factor images show FRET occurrence and subsequent colocalization of 7KC and NR. CONCLUSION: This investigation established the utility of 2-photon excitation CLSM to assess colocalization of 7KC with NR by FRET and to identify and distinguish polar and neutral lipids stained by NR that accumulate from the effect of 7KC.

Using an adaptive semiautomated self-evaluated registration technique to analyze MRI data for myocardial perfusion assessment.

PURPOSE: To validate the adaptive semiautomated self-evaluated registration technique (ASSERT) followed by factor analysis of medical image sequence (FAMIS) for analyzing myocardial perfusion using magnetic resonance imaging (MRI) images. MATERIALS AND METHODS: Eleven patients having a significant stenosis of at least one coronary artery detected by coronarography were examined by thallium tomoscintigraphy and perfusion MRI (first-pass of Gd-DTPA-BMA) at rest and under pharmacologic stress. The MRI images were analyzed by ASSERT to correct for rigid motion in the acquisition plane and to reject those images that were severely deformed or acquired outside the slice plane. The images thus obtained were analyzed by FAMIS. The resulting factor images representing myocardial perfusion were read to identify the ischemic territories corresponding to left anterior descending coronary arteries and right coronary arteries. RESULTS: ASSERT allowed automatic correction for motion and the exclusion of images that could not be registered. The ischemic territories, identified from the factor images of the myocardium, agreed with those identified by coronarography and tomoscintigraphy for 20 of the 22 territories. CONCLUSION: The results demonstrate the feasibility of analyzing myocardial perfusion using MRI acquisition and treating the resulting images by ASSERT and FAMIS. Extending this method to multislice examinations will enable evaluation of the perfusion of the whole myocardium.

Distribution of injected MRI contrast agents in mouse livers studied by confocal and SIMS microscopy.

OBJECTIVE: To localize magnetic resonance imaging (MRI) contrast agents injected intravenously into mouse livers. STUDY DESIGN: Parallel studies were performed on fluorescent europium and nonfluorescent, paramagnetic gadolinium and on a product combining nanoparticles of Fe and Texas Red to obtain combined information on the distribution of these molecules inside the liver. The distribution of different superparamagnetic iron oxides was also studied because the size of these new compounds is not always convenientfor microcirculation studies. RESULTS: Europium and Texas Red can be detected by confocal microscopy. Europium, iron and gadolinium can be detected by secondary ion mass spectrometry (SIMS) microscopy. Studies confirmed the complementarity of both microscopies. They also confirmed the possibility of using europium as a model of gadolinium to analyze thefate of MRI contrast agents. CONCLUSION: The methodology can be used on mice injected intravenously and analyzed by confocal and SIMS microscopy to localize MRI contrast agents inside cellular and tissue specimens of mice.

Improved confocal characterization of targets in nuclei of cytogenetic preparations.

OBJECTIVE: To show that cellular preparations requiring depth analysis of different domains stained by molecular cytogenetic methods (fluorescence in situ hybridization and primed in situ) can be improved by regularized factor analysis of medical image sequences (FAMIS) to isolate fluorescent probes by means of intensity depth profiles of fluorochromes, to track relevant DNA sequences (cosmids and centromeres) in cell nuclei during interphase and to improve the use of cytogenetic techniques resulting in flat preparations of whole cells that are assumed to preserve probe access to their targets. STUDY DESIGN: 3D sequences of images obtained by depth displacement in a confocal microscope were first analyzed by the FAMIS algorithm, which provides factor curves. Factor images then resulted from regularization methods that improve signal/noise ratio while preserving target contours. RESULTS: Factor curves and regularized factor images helped analyze targets inside nuclei. CONCLUSION: It is possible to process preparations containing numerous spots (even when they are on different planes) to differentiate stained targets, to investigate depth differences and to improve visualization and detection.