FISHji: new ImageJ macros for the quantification of fluorescence in epifluorescence images

Fluorescence in situ hybridization (FISH) is based on the use of fluorescent staining dyes, however, the signal intensity of the images obtained by microscopy is seldom quantified with accuracy by the researcher. The development of innovative digital image processing programs and tools has been trying to overcome this problem, however, the determination of fluorescent intensity in microscopy images still has issues due to the lack of precision in the results and the complexity of existing software. This work presents FISHji, a set of new ImageJ methods for automated quantification of fluorescence in images obtained by epifluorescence microscopy. To validate the methods, results obtained by FISHji were compared with results obtained by flow cytometry. The mean correlation between FISHji and flow cytometry was high and significant, showing that the imaging methods are able to accurately assess the signal intensity of fluorescence images. FISHji are available for non-commercial use at http://paginas.fe.up.pt/nazevedo/.

Konstruktive Exploration räumlicher Daten

Augmented reality, haptic feedback, force feedback, image processing, assistive technologies, GIS

Hochdurchsatz-Screeningsystem zur Objekterkennung in Mikroskop-Farbbildern im Rahmen der Analyse pflanzlicher Pathogenresistenz

Color image processing, pattern recognition, machine vision, application

Automatisierte Hardware-Software Partitionierung am Beispiel eines eingebetteten, echtzeitfähigen Stereobildanalysesystems in Kraftfahrzeugen

Hardware-Software Co-Design, Simulated Annealing, Real-Time Image Processing, Automated Hardware-Software Partitioning

Metodologia a seguir per la reconstrucció d’imatges mèdiques i la seva transformació en geometries mallades per a l’ús computacional

Estudi elaborat a partir d’una estada a l'Imperial College of London, Gran Bretanya, entre setembre i desembre 2006. Disposar d'una geometria bona i ben definida és essencial per a poder resoldre eficientment molts dels models computacionals i poder obtenir uns resultats comparables a la realitat del problema. La reconstrucció d'imatges mèdiques permet transformar les imatges obtingudes amb tècniques de captació a geometries en formats de dades numèriques . En aquest text s'explica de forma qualitativa les diverses etapes que formen el procés de reconstrucció d'imatges mèdiques fins a finalment obtenir una malla triangular per a poder‐la processar en els algoritmes de càlcul. Aquest procés s'inicia a l'escàner MRI de The Royal Brompton Hospital de Londres del que s'obtenen imatges per a després poder‐les processar amb les eines CONGEN10 i SURFGEN per a un entorn MATLAB. Aquestes eines les han desenvolupat investigadors del Bioflow group del departament d'enginyeria aeronàutica del Imperial College of London i en l'ultim apartat del text es comenta un exemple d'una artèria que entra com a imatge mèdica i surt com a malla triangular processable amb qualsevol programari o algoritme que treballi amb malles.

Does abdominoplasty with liposuction of the love handles yield a shorter scar? An analysis with abdominal 3D laser scanning.

The aim of this study was to evaluate the combination of abdominoplasty with liposuction of both flanks with regards to length of scar, complications, and patient's satisfaction. A retrospective analysis of 35 patients who underwent esthetic abdominoplasty at our institution between 2002 and 2004 was performed. Thirteen patients underwent abdominoplasty with liposuction of both flanks, 22 patients underwent conventional abdominoplasty. Liposuction of the flanks did not increase the rate of complications of the abdominoplasty procedures. We found a tendency toward shorter scars in patients who underwent abdominoplasty combined with liposuction of the flanks. Implementation of 3-dimensional laser surface scanning to objectify the postoperative outcomes, documented a comparable degree of flatness of the achieved body contouring in both procedures. 3-dimensional laser surface scanning can be a valuable tool to objectify assessment of postoperative results.

Reconocimiento de objetos multi-clase basado en descriptores de forma

Este trabajo presenta un sistema para detectar y clasificar objetos binarios según la forma de éstos. En el primer paso del procedimiento, se aplica un filtrado para extraer el contorno del objeto. Con la información de los puntos de forma se obtiene un descriptor BSM con características altamente descriptivas, universales e invariantes. En la segunda fase del sistema se aprende y se clasifica la información del descriptor mediante Adaboost y Códigos Correctores de Errores. Se han usado bases de datos públicas, tanto en escala de grises como en color, para validar la implementación del sistema diseñado. Además, el sistema emplea una interfaz interactiva en la que diferentes métodos de procesamiento de imágenes pueden ser aplicados.

Fusion of Multi-Atlas Segmentations with Spatial Distribution Modeling

In recent years, multi-atlas fusion methods have gainedsignificant attention in medical image segmentation. Inthis paper, we propose a general Markov Random Field(MRF) based framework that can perform edge-preservingsmoothing of the labels at the time of fusing the labelsitself. More specifically, we formulate the label fusionproblem with MRF-based neighborhood priors, as an energyminimization problem containing a unary data term and apairwise smoothness term. We present how the existingfusion methods like majority voting, global weightedvoting and local weighted voting methods can be reframedto profit from the proposed framework, for generatingmore accurate segmentations as well as more contiguoussegmentations by getting rid of holes and islands. Theproposed framework is evaluated for segmenting lymphnodes in 3D head and neck CT images. A comparison ofvarious fusion algorithms is also presented.

Sparse regularization for fiber ODF reconstruction: from the suboptimality of ℓ2 and ℓ1 priors to ℓ0.

Diffusion MRI is a well established imaging modality providing a powerful way to probe the structure of the white matter non-invasively. Despite its potential, the intrinsic long scan times of these sequences have hampered their use in clinical practice. For this reason, a large variety of methods have been recently proposed to shorten the acquisition times. Among them, spherical deconvolution approaches have gained a lot of interest for their ability to reliably recover the intra-voxel fiber configuration with a relatively small number of data samples. To overcome the intrinsic instabilities of deconvolution, these methods use regularization schemes generally based on the assumption that the fiber orientation distribution (FOD) to be recovered in each voxel is sparse. The well known Constrained Spherical Deconvolution (CSD) approach resorts to Tikhonov regularization, based on an ℓ(2)-norm prior, which promotes a weak version of sparsity. Also, in the last few years compressed sensing has been advocated to further accelerate the acquisitions and ℓ(1)-norm minimization is generally employed as a means to promote sparsity in the recovered FODs. In this paper, we provide evidence that the use of an ℓ(1)-norm prior to regularize this class of problems is somewhat inconsistent with the fact that the fiber compartments all sum up to unity. To overcome this ℓ(1) inconsistency while simultaneously exploiting sparsity more optimally than through an ℓ(2) prior, we reformulate the reconstruction problem as a constrained formulation between a data term and a sparsity prior consisting in an explicit bound on the ℓ(0)norm of the FOD, i.e. on the number of fibers. The method has been tested both on synthetic and real data. Experimental results show that the proposed ℓ(0) formulation significantly reduces modeling errors compared to the state-of-the-art ℓ(2) and ℓ(1) regularization approaches.

Three-dimensional cholangio-spiral CT demonstration of a post-traumatic bile leak in a child.

Bilioma is a rare complication of traumatic liver injury, and the precise site of bile leak is often difficult to demonstrate with a non-invasive technique. We report a case of post-traumatic bile leak in a 15-year-old girl in whom spiral CT after intravenous cholangiography allowed excellent preoperative demonstration of the extent of the liver rupture and an exact location of the bile leak. We think that spiral-CT cholangiography could be an accurate, non-invasive technique to investigate the biliary system in cases of paediatric liver trauma.

Reliable acetabular cup orientation with a new gravity-assisted guidance system.

Acetabular cup orientation is a key factor determining hip stability, and standard mechanical guides have shown little help in improving alignment. An in vitro study was carried out to compare the accuracy and precision of a new gravity-assisted guidance system with a standard mechanical guide. Three hundred ten cups were impacted by 5 surgeons, and the final cup orientation was measured. With the new guide, the average error in anteversion was 0.4 degrees , compared with 10.4 degrees with the standard guide and 0.3 degrees and -4.7 degrees , respectively, for abduction angles. The average time required for orienting the cups was similar for both guides. The accuracy and reproducibility obtained with the new guide were better (P < .0001). These good results would require a clinical validation.

Segmentation of brain structures in presence of a space-occupying lesion.

Brain deformations induced by space-occupying lesions may result in unpredictable position and shape of functionally important brain structures. The aim of this study is to propose a method for segmentation of brain structures by deformation of a segmented brain atlas in presence of a space-occupying lesion. Our approach is based on an a priori model of lesion growth (MLG) that assumes radial expansion from a seeding point and involves three steps: first, an affine registration bringing the atlas and the patient into global correspondence; then, the seeding of a synthetic tumor into the brain atlas providing a template for the lesion; finally, the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. The method was applied on two meningiomas inducing a pure displacement of the underlying brain structures, and segmentation accuracy of ventricles and basal ganglia was assessed. Results show that the segmented structures were consistent with the patient's anatomy and that the deformation accuracy of surrounding brain structures was highly dependent on the accurate placement of the tumor seeding point. Further improvements of the method will optimize the segmentation accuracy. Visualization of brain structures provides useful information for therapeutic consideration of space-occupying lesions, including surgical, radiosurgical, and radiotherapeutic planning, in order to increase treatment efficiency and prevent neurological damage.

Evaluación de la regeneración ósea mediante procesado de imagen

La regeneració òssia és un procés estudiat per experts de tot el món. Aquests experts estudien materials capaços d’accelerar el procés de formació de teixit ossi en zones on s’han produït defectes ossis. Després d’un determinat període de temps de l’aplicació dels materials d’estudi en la zona on hi havia una manca de teixit ossi, s’obtenen imatges d’aquesta zona on l’expert mitjançant l’ inspecció visual d’aquestes imatges avalua si l’os s’ha regenerat bé o no. El problema d’aquest mètode d’avaluació es que requereix d’un expert on la valoració d’aquest és subjectiva i difícil de quantificar, el que pot provocar que hi hagi discordança entre experts. Amb la finalitat de aprofitar les imatges en que es basa l’expert per avaluar la capacitat de regeneració òssia dels materials d’estudi es proposa realitzar un anàlisi quantitatiu de la regeneració òssia basat en el processament d’imatge. L’algorisme dissenyat es capaç de classificar imatges de la mandíbula en: imatges de regeneració bona i dolenta mitjançant la parametrització de l’histograma de nivells de grisos de la imatge, solucionant la falta d’objectivitat del mètode d’avaluació de la regeneració òssia i la necessitat d’un expert per realitzar-la.

Double-oblique free-breathing high resolution three-dimensional coronary magnetic resonance angiography.

OBJECTIVES: The goal of the present study was to develop a strategy for three-dimensional (3D) volume acquisition along the major axes of the coronary arteries. BACKGROUND: For high-resolution 3D free-breathing coronary magnetic resonance angiography (MRA), coverage of the coronary artery tree may be limited due to excessive measurement times associated with large volume acquisitions. Planning the 3D volume along the major axis of the coronary vessels may help to overcome such limitations. METHODS: Fifteen healthy adult volunteers and seven patients with X-ray angiographically confirmed coronary artery disease underwent free-breathing navigator-gated and corrected 3D coronary MRA. For an accurate volume targeting of the high resolution scans, a three-point planscan software tool was applied. RESULTS: The average length of contiguously visualized left main and left anterior descending coronary artery was 81.8 +/- 13.9 mm in the healthy volunteers and 76.2 +/- 16.5 mm in the patients (p = NS). For the right coronary artery, a total length of 111.7 +/- 27.7 mm was found in the healthy volunteers and 79.3 +/- 4.6 mm in the patients (p = NS). Comparing coronary MRA and X-ray angiography, a good agreement of anatomy and pathology was found in the patients. CONCLUSIONS: Double-oblique submillimeter free-breathing coronary MRA allows depiction of extensive parts of the native coronary arteries. The results obtained in patients suggest that the method has the potential to be applied in broader prospective multicenter studies where coronary MRA is compared with X-ray angiography.

Coronary MR angiography at 3T during diastole and systole

PURPOSE: To investigate the impact of end-systolic imaging on quality of right coronary magnetic resonance angiography (MRA) in comparison to diastolic and to study the effect of RR interval variability on image quality. MATERIALS AND METHODS: The right coronary artery (RCA) of 10 normal volunteers was imaged at 3T using parallel imaging (sensitivity encoding [SENSE]). Navigator-gated three-dimensional (3D) gradient echo was used three times: 1) end-systolic short acquisition (SS): 35-msec window; 2) diastolic short (DS): middiastolic acquisition using 35-msec window; and 3) diastolic long (DL): 75-msec diastolic acquisition window. Vectorcardiogram (VCG) data was used to analyze RR variability. Vessel sharpness, length, and diameter were compared to each other and correlated with RR variability. Blinded qualitative image scores of the images were compared. RESULTS: Quantitative and qualitative parameters were not significantly different and showed no significant correlation with RR variability. CONCLUSION: Imaging the RCA at 3T during the end-systolic rest period using SENSE is possible without significant detrimental effect on image quality. Breaking away from the standard of imaging only during diastole can potentially improve image quality in tachycardic patients or used for simultaneous imaging during both periods in a single scan.