3D object segmentation
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Background: Breast cancer is one of the leading cancers in woman worldwide both in developed and developing nations as per the records from World Health Organization. Many studies have shown that mammography is very effective tool for the breast cancer diagnosis. Mass segmentation plays an important step for the cancer detection. Objective: The objective of the proposed method is to segment the mass and to classify the mass with high accuracy. Methods: The segmentation includes two main steps. First, a rough initial segmentation through iterative thresholding, and second, an active contour based segmentation. The relevant statistical features are extracted and the classification is done by using Adaptive Neuro Fuzzy Inference System (ANFIS). Results: The proposed mass detection scheme achieves sensitivity of 87.5% and specificity of 100% for a set of twenty two images. The overall segmentation accuracy obtained is 91.30%. Conclusions: This work appears to be of high clinical significance since the mass detection plays an important role in diagnosis of breast cancer.
Úvod: CT angiokardiografia (CTA ) je moderná zobrazovacia metóda využívaná na detailné zobrazovanie kardiovaskulárnych štruktúr u pediatrických pacientov s vrodenými či získanými ochoreniami srdca. Najprehľadnejšou formou zobrazovania v detskej kardiológii v súčasnosti sú 3D virtuálne modely srdca vyrekonštruované z CT dát. Metódy a ciele práce: Retrospektívna analýza CTA vyšetrení zrealizovaných v období 10 / 2021 – 09 / 2022 u pacientov sledovaných v Detskom kardiocentre, NÚSCH, a. s., Bratislava. Cieľom štúdie bolo získať komplexný prehľad o realizovaných CTA vyšetreniach v období 1 roka. Vyhodnocované boli indikácie CTA ako aj prínos výsledkov CTA pre následný klinický manažment pacientov. Zároveň boli hodnotené vysegmentované 3D virtuálne modely z hľadiska ich počtu, indikácií na ich výrobu ako aj ich klinického prínosu. Výsledky: Počas 1-ročného obdobia bolo zrealizovaných 313 CTA vyšetrení u 280 pacientov. Iba v 2 / 313 (0,6%) prípadoch bol výsledok CTA vyšetrenia pre obrazové artefakty nedostatočne hodnotiteľný. V ostatných 311 / 313 (99,4%) prípadoch bolo CTA zobrazenie kardiovaskulárnych štruktúr dostatočne kvalitné a vyšetrenie tak bolo prínosné pre optimalizáciu ďalšieho klinického manažmentu pacientov. Výstupy CTA vyšetrení boli nasledovné: kardiochirurgický výkon: 118 / 313 (37,7%), katetrizačný intervenčný výkon: 42 / 313 (13,4%), trombolýza: 5 / 313 (1,6%), zmena antikoagulačnej liečby: 1 / 313 (0,3%), kryoablačná liečba: 1 / 313 (0,3%), paliatívna liečba: 9 / 313 (2,9%), konzervatívny postup bez nutnosti intervencie či zmeny liečby: 134 / 313 (42,8%). 3D virtuálne modely boli vytvorené v 16 prípadoch. Na základe ich analýzy boli rozhodnutia pre následný klinický manažment nasledovné: 14 / 16 (88%) kardiochirurgický výkon: dvojkomorové riešenie, 1 / 16 (6,3%) kardiochirurgický výkon: jednokomorové riešenie, a 1 / 16 (6,3%) paliatívna liečba. Záver: CTA je v rámci pediatrickej kardiológie stále viac využívaným zobrazovacím vyšetrením zameraným na hodnotenie anatómie kardiovaskulárneho systému najmä u pacientov s vrodenými chybami srdca (VCC). Virtuálne 3D modely srdca sú v súčasnosti najmodernejšou formou anatomického zobrazovania komplexných VCC. Výsledky našej štúdie preukázali, že využívanie CTA ako aj virtuálnych 3D modelov významne prispieva k k optimalizácii klinického manažmentu detských pacientov s ochoreniami srdca.
Introduction: CT angiocardiography (CTA ) is a modern imaging method used for detailed imaging of cardiovascular structures in pediatric patients with congenital or acquired heart diseases. 3D virtual heart models reconstructed from CT data are currently the most detailed form of anatomical imaging in pediatric cardiology. Methods and objectives: Retrospective analysis of CTA examinations performed in patients treated at the Pediatric Cardiac Center, Bratislava, between 10 / 2021 – 09 / 2022. The goal of the study was to obtain a comprehensive overview of CTA examinations performed during a 1 year period. CTA indications as well as the contribution of CTA results to the subsequent clinical management of patients were evaluated. At the same time, segmented 3D virtual models were evaluated in terms of their number, indications for their reconstructions, and as well as their clinical benefit. Results: 313 CTA examinations were performed in 280 patients in 1-year period. Only in 2 out of 313 (0.6%) cases were the results of the CTA examination insufficient due to image artifacts. In the other 311 / 313 (99.4%) cases, the CTA imaging of cardiovascular structures was of sufficient quality, and the examinations were beneficial for optimization of further clinical management of patients. The results of CTA examinations were as follows: cardiac surgery: 118 / 313 (37.7%), catheterizat intervention: 42 / 313 (13.4%), thrombolysis: 5 / 313 (1.6%), change of anticoagulation therapy: 1 / 313 (0.3%), cryoablation treatment: 1 / 313 (0.3%), palliative treatment: 9 / 313 (2.9%), conservative procedure without the need for intervention or treatment change: 134 / 313 (42 .8%). 3D virtual models were created in 16 cases. Based on analysis of the models, the decisions for subsequent clinical management were as follows: 14 / 16 (88%) cardiac surgery: biventricular circulation, 1 / 16 (6.3%) cardiac surgery: single-ventricle circulation, and 1 / 16 (6.3%) palliative treatment. Conclusion: CTA is an increasingly used imaging method in pediatric cardiology aimed at evaluating of the cardiovascular system anatomy, especially in patients with congenital heart defects (CHD). Virtual 3D heart models are currently the most recent form of anatomical imaging of complex CHDs. The results of our study demonstrated that the use of CTA as well as virtual 3D models significantly contribute to the optimization of the clinical management of pediatric patients with cardiac diseases.
- MeSH
- angiokardiografie * metody MeSH
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- modely kardiovaskulární * MeSH
- novorozenec MeSH
- předškolní dítě MeSH
- retrospektivní studie MeSH
- virtuální realita MeSH
- vrozené srdeční vady diagnostické zobrazování MeSH
- zobrazování trojrozměrné MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- přehledy MeSH
- Geografické názvy
- Slovenská republika MeSH
Automatic detection and segmentation of biological objects in 2D and 3D image data is central for countless biomedical research questions to be answered. While many existing computational methods are used to reduce manual labeling time, there is still a huge demand for further quality improvements of automated solutions. In the natural image domain, spatial embedding-based instance segmentation methods are known to yield high-quality results, but their utility to biomedical data is largely unexplored. Here we introduce EmbedSeg, an embedding-based instance segmentation method designed to segment instances of desired objects visible in 2D or 3D biomedical image data. We apply our method to four 2D and seven 3D benchmark datasets, showing that we either match or outperform existing state-of-the-art methods. While the 2D datasets and three of the 3D datasets are well known, we have created the required training data for four new 3D datasets, which we make publicly available online. Next to performance, also usability is important for a method to be useful. Hence, EmbedSeg is fully open source (https://github.com/juglab/EmbedSeg), offering (i) tutorial notebooks to train EmbedSeg models and use them to segment object instances in new data, and (ii) a napari plugin that can also be used for training and segmentation without requiring any programming experience. We believe that this renders EmbedSeg accessible to virtually everyone who requires high-quality instance segmentations in 2D or 3D biomedical image data.
- MeSH
- algoritmy * MeSH
- lidé MeSH
- mikroskopie * metody MeSH
- počítačové zpracování obrazu metody MeSH
- zobrazování trojrozměrné metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Image cytometry still faces the problem of the quality of cell image analysis results. Degradations caused by cell preparation, optics, and electronics considerably affect most 2D and 3D cell image data acquired using optical microscopy. That is why image processing algorithms applied to these data typically offer imprecise and unreliable results. As the ground truth for given image data is not available in most experiments, the outputs of different image analysis methods can be neither verified nor compared to each other. Some papers solve this problem partially with estimates of ground truth by experts in the field (biologists or physicians). However, in many cases, such a ground truth estimate is very subjective and strongly varies between different experts. To overcome these difficulties, we have created a toolbox that can generate 3D digital phantoms of specific cellular components along with their corresponding images degraded by specific optics and electronics. The user can then apply image analysis methods to such simulated image data. The analysis results (such as segmentation or measurement results) can be compared with ground truth derived from input object digital phantoms (or measurements on them). In this way, image analysis methods can be compared with each other and their quality (based on the difference from ground truth) can be computed. We have also evaluated the plausibility of the synthetic images, measured by their similarity to real image data. We have tested several similarity criteria such as visual comparison, intensity histograms, central moments, frequency analysis, entropy, and 3D Haralick features. The results indicate a high degree of similarity between real and simulated image data.
- MeSH
- algoritmy MeSH
- buněčné jadérko ultrastruktura MeSH
- buněčné jádro MeSH
- fantomy radiodiagnostické MeSH
- fluorescenční mikroskopie metody MeSH
- granulocyty cytologie MeSH
- HL-60 buňky MeSH
- lidé MeSH
- mikrosféry MeSH
- obrazová cytometrie metody MeSH
- zobrazování trojrozměrné metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.
- MeSH
- algoritmy * MeSH
- analýza hlavních komponent * MeSH
- buňky Hep G2 MeSH
- DNA vazebné proteiny metabolismus MeSH
- fluorescenční mikroskopie * MeSH
- konformace nukleové kyseliny MeSH
- lidé MeSH
- mitochondriální DNA chemie metabolismus MeSH
- mitochondriální proteiny metabolismus MeSH
- molekulární modely MeSH
- zobrazování trojrozměrné * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Quantification of the structure and composition of biomaterials using micro-CT requires image segmentation due to the low contrast and overlapping radioopacity of biological materials. The amount of bias introduced by segmentation procedures is generally unknown. We aim to develop software that generates three-dimensional models of fibrous and porous structures with known volumes, surfaces, lengths, and object counts in fibrous materials and to provide a software tool that calibrates quantitative micro-CT assessments. Virtual image stacks were generated using the newly developed software TeIGen, enabling the simulation of micro-CT scans of unconnected tubes, connected tubes, and porosities. A realistic noise generator was incorporated. Forty image stacks were evaluated using micro-CT, and the error between the true known and estimated data was quantified. Starting with geometric primitives, the error of the numerical estimation of surfaces and volumes was eliminated, thereby enabling the quantification of volumes and surfaces of colliding objects. Analysis of the sensitivity of the thresholding upon parameters of generated testing image sets revealed the effects of decreasing resolution and increasing noise on the accuracy of the micro-CT quantification. The size of the error increased with decreasing resolution when the voxel size exceeded 1/10 of the typical object size, which simulated the effect of the smallest details that could still be reliably quantified. Open-source software for calibrating quantitative micro-CT assessments by producing and saving virtually generated image data sets with known morphometric data was made freely available to researchers involved in morphometry of three-dimensional fibrillar and porous structures in micro-CT scans.
BACKGROUND: The presented study investigates the application of bi-arterial 3D printed models to guide transseptal puncture (TSP) in left atrial appendage closure (LAAC). AIMS: The objectives are to (1) test the feasibility of 3D printing (3DP) for TSP guidance, (2) analyse the distribution of the optimal TSP locations, and (3) define a CT-derived 2D parameter suitable for predicting the optimal TSP locations. METHODS: Preprocedural planning included multiplanar CT reconstruction, 3D segmentation, and 3DP. TSP was preprocedurally simulated in vitro at six defined sites. Based on the position of the sheath, TSP sites were classified as optimal, suboptimal, or nonoptimal. The aim was to target the TSP in the recommended position during the procedure. Procedure progress was assessed post hoc by the operator. RESULTS: Of 68 screened patients, 60 patients in five centers (mean age of 74.68 ± 7.64 years, 71.66% males) were prospectively analyzed (3DP failed in one case, and seven patients did not finally undergo the procedure). In 55 patients (91.66%), TSP was performed in the optimal location as recommended by the 3DP. The optimal locations for TSP were postero-inferior in 45.3%, mid-inferior in 45.3%, and antero-inferior in 37.7%, with a mean number of optimal segments of 1.34 ± 0.51 per patient. When the optimal TSP location was achieved, the procedure was considered difficult in only two (3.6%) patients (but in both due to complicated LAA anatomy). Comparing anterior versus posterior TSP in 2D CCT, two parameters differed significantly: (1) the angle supplementary to the LAA ostium and the interatrial septum angle (160.83° ± 9.42° vs. 146.49° ± 8.67°; p = 0.001), and (2) the angle between the LAA ostium and the mitral annulus (95.02° ± 3.73° vs. 107.38° ± 6.76°; p < 0.001), both in the sagittal plane. CONCLUSIONS: In vitro TSP simulation accurately determined the optimal TSP locations for LAAC and facilitated the procedure. More than one-third of the optimal TSP sites were anterior.
- MeSH
- 3D tisk MeSH
- fibrilace síní * terapie chirurgie MeSH
- lidé MeSH
- počítačová rentgenová tomografie MeSH
- punkce metody MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- síňové ouško * diagnostické zobrazování chirurgie MeSH
- výsledek terapie MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
INTRODUCTION AND OBJECTIVES: Pathologic intimal thickening (PIT) has been considered a benign plaque phenotype. We report plaque phenotypic changes in a baseline/follow-up intravascular ultrasound-based virtual histology study. METHODS: A total of 61 patients with stable coronary artery disease were analyzed from the HEAVEN trial (89 patients randomized between routine statin therapy vs atorvastatin 80mg and ezetimibe 10mg) with serial intravascular ultrasound imaging of nonculprit vessels. We compared changes in 693 baseline and follow-up 5-mm long segments in a novel risk score, Liverpool Active Plaque Score (LAPS), plaque parameters, and plaque composition. RESULTS: The PIT showed the highest increase of risk score and, with fibrous plaque, also the LAPS. Necrotic core (NC) abutting to the lumen increased in PIT (22 ± 51.7; P = .0001) and in fibrous plaque (17.9 ± 42.6; P = .004) but decreased in thin cap fibroatheroma (TCFA) (⿿15.14 ± 52.2; P = .001). The PIT was the most likely of all nonthin cap fibroatheroma plaque types to transform into TCFA at follow-up (11% of all TCFA found during follow-up and 35.9% of newly-developed TCFA), but showed (together with fibrous plaque) the lowest stability during lipid-lowering therapy (24.7% of PIT remained PIT and 24.5% of fibrous plaque remained fibrous plaque). CONCLUSIONS: Over the 1-year follow-up, PIT was the most dynamic of the plaque phenotypes and was associated with an increase of risk score and LAPS (together with fibrous plaque), NC percentage (together with fibrous plaque) and NC abutting to the lumen, despite a small reduction of plaque volume during lipid-lowering therapy. The PIT was the main source for new TCFA segments.
- MeSH
- anticholesteremika aplikace a dávkování MeSH
- aterosklerotický plát krev diagnóza farmakoterapie MeSH
- atorvastatin aplikace a dávkování MeSH
- časové faktory MeSH
- ezetimib aplikace a dávkování MeSH
- intervenční ultrasonografie metody MeSH
- kombinovaná farmakoterapie MeSH
- koronární cévy diagnostické zobrazování MeSH
- LDL-cholesterol krev MeSH
- lidé středního věku MeSH
- lidé MeSH
- následné studie MeSH
- nemoci koronárních tepen krev diagnóza farmakoterapie MeSH
- progrese nemoci MeSH
- stupeň závažnosti nemoci MeSH
- uživatelské rozhraní počítače * MeSH
- vztah mezi dávkou a účinkem léčiva MeSH
- zobrazování trojrozměrné MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- randomizované kontrolované studie MeSH
OBJECTIVES: The diploic channels appear to be more developed in humans than in nonhuman primates, suggesting they may be relevant in evolutionary biology. This study is aimed at providing a segmentation procedure for diploic channels and CT analysis, a quantitative description of their variation in modern humans, and paleoanthropological case-studies. MATERIALS AND METHODS: CT data were used for the 2D and 3D visualization, rendering, and measure, of diploic channels in modern and fossil hominids. We analyzed 20 modern human skulls and three Neanderthals. The effect of different resolution factors was evaluated. A specific protocol was designed to segment the vascular network and localize the main branches, reducing the noise of the cancellous bone. RESULTS: We provide a quantitative description of the frontal, parietal, and occipital diploic networks in modern humans and in three Neanderthals. There is a correlation in the degree of vascularization among the different vault areas. No side differences can be detected. The diploic network is commonly connected with the meningeal artery at the temporal fossa, with the emissary veins at the occipital bone, and with the venous sinuses at the parieto-occipital areas. The channels are more developed in the parietal areas. The three Neanderthals show a vascular development, which is in the lower range of the modern human variation. CONCLUSIONS: Modern humans display a large variation in their morphological patterns, being the parietal area the most vascularized. The pattern of the diploic channels may be relevant in anthropology, medicine, and paleontology, taking into account their possible involvement in thermoregulation.
- MeSH
- antropologie fyzická MeSH
- dospělí MeSH
- lebka * anatomie a histologie krevní zásobení radiografie MeSH
- lidé MeSH
- neandertálci anatomie a histologie MeSH
- počítačová rentgenová tomografie MeSH
- zkameněliny * MeSH
- zvířata MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
OBJECTIVE: In the children born with a cleft lip, surgery is the first step in correcting the inborn anomaly. In comparison with usually made 3-month surgery, benefits of the surgery in neonates have been reported: a very good wound healing, feeding facilitation, and good socialization of a child from neonatal age. The aims of the present study were to perform cheiloplasty in early newborns affected by the total cleft lip and palate (CLP) by the technique modified to search for optimum aesthetic result, and to assess the surgery outcome from qualitative and quantitative aspects. METHODS: The operations were performed by the same surgeon in 97 neonates 1-8 days old during 2005-2008. The original technique by Tennison was modified and used. Aesthetic outcome of the surgery was evaluated according to scar visibility, and the shape and symmetry of the lip and nose. The effect of cheiloplasty on the formation of the upper jaw segments was evaluated in a sample of unilateral CLP patients using the 3D-finite element scaling analysis (FESA). We compared 3D models of dental plaster casts made prior to lip surgery (in neonates under 8 days of age) and prior to palate surgery (at 12 months of age). RESULTS: Only the children in excellent health state and without an associated inborn defect were allowed to pass the operation. There were no per-operative complications (except the correction of tracheal tube position in several cases). The parents appreciated bringing home a neonate with no visible cleft. This aspect not only facilitated baby feeding, but had important positive psycho-social impact on the whole family. The wound healing and aesthetic effect of the cheiloplasty were very good. The scar was barely visible and lip and nose were symmetric in majority of children. After lip closure, the growth and approximation of jaw segments was observed. This aspect was also associated with incisors development in the anterior portion of the segment including premaxilla. CONCLUSIONS: Our results show, that early neonatal lip surgery of CLP is promising technique with very good aesthetic results and important positive psychological impact on the child and its family.
- MeSH
- analýza metodou konečných prvků MeSH
- estetika MeSH
- jizva patologie MeSH
- lidé MeSH
- novorozenec MeSH
- počítačová simulace MeSH
- rodiče psychologie MeSH
- rozštěp rtu chirurgie MeSH
- zákroky plastické chirurgie * MeSH
- zobrazování trojrozměrné MeSH
- Check Tag
- lidé MeSH
- novorozenec MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
