Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis.

Purpose: Deformable medial modeling is an inverse skeletonization approach to representing anatomy in medical images, which can be used for statistical shape analysis and assessment of patient-specific anatomical features such as locally varying thickness. It involves deforming a pre-defined synthetic skeleton, or template, to anatomical structures of the same class. The lack of software for creating such skeletons has been a limitation to more widespread use of deformable medial modeling. Therefore, the objective of this work is to present an open-source user interface (UI) for the creation of synthetic skeletons for a range of medial modeling applications in medical imaging. Approach: A UI for interactive design of synthetic skeletons was implemented in 3D Slicer, an open-source medical image analysis application. The steps in synthetic skeleton design include importation and skeletonization of a 3D segmentation, followed by interactive 3D point placement and triangulation of the medial surface such that the desired branching configuration of the anatomical structure's medial axis is achieved. Synthetic skeleton design was evaluated in five clinical applications. Compatibility of the synthetic skeletons with open-source software for deformable medial modeling was tested, and representational accuracy of the deformed medial models was evaluated. Results: Three users designed synthetic skeletons of anatomies with various topologies: the placenta, aortic root wall, mitral valve, cardiac ventricles, and the uterus. The skeletons were compatible with skeleton-first and boundary-first software for deformable medial modeling. The fitted medial models achieved good representational accuracy with respect to the 3D segmentations from which the synthetic skeletons were generated. Conclusions: Synthetic skeleton design has been a practical challenge in leveraging deformable medial modeling for new clinical applications. This work demonstrates an open-source UI for user-friendly design of synthetic skeletons for anatomies with a wide range of topologies.

A fast phenotype approach of 3D point clouds of Pinus massoniana seedlings.

The phenotyping of Pinus massoniana seedlings is essential for breeding, vegetation protection, resource investigation, and so on. Few reports regarding estimating phenotypic parameters accurately in the seeding stage of Pinus massoniana plants using 3D point clouds exist. In this study, seedlings with heights of approximately 15-30 cm were taken as the research object, and an improved approach was proposed to automatically calculate five key parameters. The key procedure of our proposed method includes point cloud preprocessing, stem and leaf segmentation, and morphological trait extraction steps. In the skeletonization step, the cloud points were sliced in vertical and horizontal directions, gray value clustering was performed, the centroid of the slice was regarded as the skeleton point, and the alternative skeleton point of the main stem was determined by the DAG single source shortest path algorithm. Then, the skeleton points of the canopy in the alternative skeleton point were removed, and the skeleton point of the main stem was obtained. Last, the main stem skeleton point after linear interpolation was restored, while stem and leaf segmentation was achieved. Because of the leaf morphological characteristics of Pinus massoniana, its leaves are large and dense. Even using a high-precision industrial digital readout, it is impossible to obtain a 3D model of Pinus massoniana leaves. In this study, an improved algorithm based on density and projection is proposed to estimate the relevant parameters of Pinus massoniana leaves. Finally, five important phenotypic parameters, namely plant height, stem diameter, main stem length, regional leaf length, and total leaf number, are obtained from the skeleton and the point cloud after separation and reconstruction. The experimental results showed that there was a high correlation between the actual value from manual measurement and the predicted value from the algorithm output. The accuracies of the main stem diameter, main stem length, and leaf length were 93.5%, 95.7%, and 83.8%, respectively, which meet the requirements of real applications.

Edge-Supervised Linear Object Skeletonization for High-Speed Camera.

This paper presents a high-speed skeletonization algorithm for detecting the skeletons of linear objects from their binary images. The primary objective of our research is to achieve rapid extraction of the skeletons from binary images while maintaining accuracy for high-speed cameras. The proposed algorithm uses edge supervision and a branch detector to efficiently search inside the object, avoiding unnecessary computation on irrelevant pixels outside the object. Additionally, our algorithm addresses the challenge of self-intersections in linear objects with a branch detection module, which detects existing intersections and initializes new searches on emerging branches when necessary. Experiments on various binary images, such as numbers, ropes, and iron wires, demonstrated the reliability, accuracy, and efficiency of our approach. We compared the performance of our method with existing skeletonization techniques, showing its superiority in terms of speed, especially for larger image sizes.

How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques.

Computer vision technology is moving more and more towards a three-dimensional approach, and plant phenotyping is following this trend. However, despite its potential, the complexity of the analysis of 3D representations has been the main bottleneck hindering the wider deployment of 3D plant phenotyping. In this review we provide an overview of typical steps for the processing and analysis of 3D representations of plants, to offer potential users of 3D phenotyping a first gateway into its application, and to stimulate its further development. We focus on plant phenotyping applications where the goal is to measure characteristics of single plants or crop canopies on a small scale in research settings, as opposed to large scale crop monitoring in the field.

Handling Severe Intraoperative Hemorrhage and Avoiding Iatrogenic Stroke During Brain Tumor Surgery: Techniques for Prevention of Hemorrhagic and Ischemic Complications.

BACKGROUND: Nationwide databases show that iatrogenic stroke and postoperative hematoma are among the commonest complications in brain tumor surgery, with a 10-year incidence of 16.3/1000 and 10.3/1000, respectively. However, techniques for handling severe intraoperative hemorrhage and dissecting, preserving, or selectively obliterating vessels traversing the tumor are sparse in the literature. METHODS: Records of the senior author's intraoperative techniques during severe haemorrhage and vessel preservation were reviewed and analyzed. Intraoperative media demonstrations of key techniques were collected and edited. In parallel, a literature search investigating technique description in handling severe intraoperative hemorrhage and vessel preservation in tumor surgery was undertaken. Histologic, anesthetic, and pharmacologic prerequisites of significant hemorrhagic complications and hemostasis were analyzed. RESULTS: The senior author's techniques for arterial and venous skeletonization, temporary clipping with cognitive or motor mapping, and ION monitoring were categorized. Vessels interfacing with tumor are labeled intraoperatively as supplying/draining the tumor, or traversing en passant, while supplying/draining functional neural tissue. Intraoperative techniques of differentiation were analyzed and illustrated. Literature search found 2 vascular-related complication domains in tumor surgery: perioperative management of excessively vascular intraparenchymal tumors and lack of intraoperative techniques and decision processes for dissecting and preserving vessels interfacing or traversing tumors. CONCLUSIONS: Literature searches showed a dearth of complication-avoidance techniques in tumor-related iatrogenic stroke, despite its high prevalence. A detailed preoperative and intraoperative decision process was provided along with a series of case illustrations and intraoperative videos showing the techniques required to reduce intraoperative stroke and associated morbidity addressing a void in complication avoidance of tumor surgery.

Anatomists' uses of human skeletons: Ethical issues associated with the India bone trade and anonymized archival collections.

Concerns have recently been expressed about the continuing availability of human bones from India, obtained originally for educational purposes but lacking the requisite informed consent that would be expected today. More generally, a broader claim is being made, namely, that the practice of using any unconsented bones in educational settings is unethical and should cease. These calls, in turn, raise broader issues regarding the availability of anonymous archival collections in anatomy museums. Although this debate centers on undergraduate anatomy teaching, much anthropological research utilizes human remains of past populations for which there can have been no consent. A suggested alternative for undergraduate teaching is the use of 3D images of human bones, rather than the bones themselves. In addressing these issues, the background to the India bone trade is assessed, and the year 1985 is pinpointed as having significant ethical weight. The cultural and ethical interests inherent in studying archival anonymous skeletal material are weighed against indiscriminate reburial. Although any use of unconsented material represents ethical compromise, account should be taken of changing ethical expectations with time. It is concluded that: there is no justification for repatriation or disposal of all bones for which specific informed consent has not been obtained; continued use of anonymous archival human bones in a professional setting is acceptable, even in the absence of informed consent, with the proviso that there are no culturally relevant groups seeking repatriation; the continued existence of bones in long-standing private collections cannot be justified since it amounts to long-term storage with no identified goals; the notion that 3D images are an ethically superior alternative to actual human bones is unsustainable, since there is an intimate connection between the bones and the 3D images.

Blood flow characteristics of the bilateral internal thoracic artery: implications of optimal graft configuration for coronary artery bypass grafting to maximize blood supply.

PURPOSE: There is controversy regarding which internal thoracic artery (ITA) should be anastomosed to the left anterior descending artery (LAD). Here, we propose an optimal graft design based on measurement of blood flow in the ITA. METHODS: Sixty-one patients (53 men, median age 68 [62-75] years) undergoing first elective coronary artery bypass grafting were enrolled. Fifty-seven left ITAs (LITAs) and 28 right ITAs (RITAs) were harvested in either a semi-skeletonized manner using a harmonic scalpel covered with papaverine-soaked gauze (group-A, n = 45) or a fully skeletonized manner using electrocautery with intraluminal papaverine injection (group-B, n = 41). Free flow of 33 ITAs was measured after pharmacological dilatation and in situ ITA-LAD flow was measured in 59 patients by transit-time flowmetry. RESULTS: RITA and LITA free flow were 147.0 [87.8-213.0] mL/min and 108.0 [90.0-144.0] mL/min, respectively (P = 0.199). The group-B had significantly higher ITA free flow (135.0 [102.0-171.0] mL/min) than group-A (63.0 [36.0-96.0] mL/min, P = 0.009). In 13 patients with bilateral ITA harvesting, free flow of the RITA (138.0 [79.5-204.0] mL/min) was also significantly higher than the LITA (102.0 [81.0-138.0] mL/min, P = 0.046). There was no significant difference between RITA and LITA flow anastomosed to the LAD. The group-B had significantly higher ITA-LAD flow (56.5 [32.3-73.6] mL/min) than group-A (40.9 [20.1-53.7] mL/min, P = 0.023). CONCLUSION: RITA provides significantly higher free flow than LITA but similar blood flow to the LAD. Full skeletonization with intraluminal papaverine injection maximizes both free flow and ITA-LAD flow.

Igneous: Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling.

Three-dimensional electron microscopy images of brain tissue and their dense segmentations are now petascale and growing. These volumes require the mass production of dense segmentation-derived neuron skeletons, multi-resolution meshes, image hierarchies (for both modalities) for visualization and analysis, and tools to manage the large amount of data. However, open tools for large-scale meshing, skeletonization, and data management have been missing. Igneous is a Python-based distributed computing framework that enables economical meshing, skeletonization, image hierarchy creation, and data management using cloud or cluster computing that has been proven to scale horizontally. We sketch Igneous's computing framework, show how to use it, and characterize its performance and data storage.

Four Severity Levels for Grading the Tortuosity of a Retinal Fundus Image.

Hypertensive retinopathy severity classification is proportionally related to tortuosity severity grading. No tortuosity severity scale enables a computer-aided system to classify the tortuosity severity of a retinal image. This work aimed to introduce a machine learning model that can identify the severity of a retinal image automatically and hence contribute to developing a hypertensive retinopathy or diabetic retinopathy automated grading system. First, the tortuosity is quantified using fourteen tortuosity measurement formulas for the retinal images of the AV-Classification dataset to create the tortuosity feature set. Secondly, a manual labeling is performed and reviewed by two ophthalmologists to construct a tortuosity severity ground truth grading for each image in the AV classification dataset. Finally, the feature set is used to train and validate the machine learning models (J48 decision tree, ensemble rotation forest, and distributed random forest). The best performance learned model is used as the tortuosity severity classifier to identify the tortuosity severity (normal, mild, moderate, and severe) for any given retinal image. The distributed random forest model has reported the highest accuracy (99.4%) compared to the J48 Decision tree model and the rotation forest model with minimal least root mean square error (0.0000192) and the least mean average error (0.0000182). The proposed tortuosity severity grading matched the ophthalmologist's judgment. Moreover, detecting the tortuosity severity of the retinal vessels', optimizing vessel segmentation, the vessel segment extraction, and the created feature set have increased the accuracy of the automatic tortuosity severity detection model.

Lymphadenectomy with venation is preferred compared to skeletonization for patients with rectal and sigmoid colon cancer: a retrospective cohort study.

Background: For patients with rectal and sigmoid colon cancer, dissecting No. 253 lymph nodes and preserving the left colic artery are the essentials of radical surgery. In clinical work, some surgeons prefer to dissect lymph nodes with skeletonization, believing that lymph nodes can be dissected completely by this method, while other surgeons prefer to dissect lymph nodes with venation. They believe that their method can not only dissect lymph nodes completely but also ensure the safety of patients. This study aimed to investigate whether lymphadenectomy with skeletonization is superior to lymphadenectomy with venation for patients with rectal and sigmoid colon cancer. Methods: We performed a retrospective cohort study between August, 2017 and October, 2019 at the Department of General Surgery, the Affiliated Hospital of Nanjing University Medical School. The inclusion criteria were as follows: diagnosed as rectum or sigmoid colon adenocarcinoma by electronic colonoscopy and histopathology; 18-80 years of age; underwent radical resection. The exclusion criteria were as follows: received neoadjuvant therapy before surgery; combined with distant metastasis. According to the method of lymph node dissection, patients were divided into the skeletonization group and venation group. We then compared the curative effect and safety between the 2 groups. Results: A total of 211 patients were recruited in this retrospective study and assigned as follows: 62 cases to the skeletonization group and 149 patients to the venation group. There were no statistical differences in the total number of lymph nodes (P=0.082), number of positive lymph nodes (P=0.097), total number of No. 253 lymph nodes (P=0.096), number of positive No. 253 lymph nodes (P=0.813), and nodal staging (P=0.254) between the 2 groups. However, the amount of bleeding in the skeletonization group was significantly higher than that in the venation group (P≤0.001), and the operation time in the skeletonization group was also significantly longer than that in the venation group (P≤0.001). Conclusions: Lymphadenectomy with venation is preferred in the radical resection of patients with rectal and sigmoid colon cancer.

Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics.

Morphological analysis of protein channels is a key step for a thorough understanding of their biological function and mechanism. In this respect, molecular dynamics (MD) is a very powerful tool, enabling the description of relevant biological events at the atomic level, which might elude experimental observations, and pointing to the molecular determinants thereof. In this work, we present a computational geometry-based approach for the characterization of the shape and dynamics of biological ion channels or pores to be used in combination with MD trajectories. This technique relies on the earliest works of Edelsbrunner and on the NanoShaper software, which makes use of the alpha shape theory to build the solvent-excluded surface of a molecular system in an aqueous solution. In this framework, a channel can be simply defined as a cavity with two entrances on the opposite sides of a molecule. Morphological characterization, which includes identification of the main axis, the corresponding local radius, and the detailed description of the global shape of the cavity, is integrated with a physico-chemical description of the surface facing the pore lumen. Remarkably, the possible existence or temporary appearance of fenestrations from the channel interior towards the outer lipid matrix is also accounted for. As a test case, we applied the present approach to the analysis of an engineered protein channel, the mechanosensitive channel of large conductance.

First Characterization of Human Dermal Fibroblasts Showing a Decreased Xylosyltransferase-I Expression Induced by the CRISPR/Cas9 System.

BACKGROUND: Xylosyltransferases-I and II (XT-I and XT-II) catalyze the initial and rate limiting step of the proteoglycan (PG) biosynthesis and therefore have an import impact on the homeostasis of the extracellular matrix (ECM). The reason for the occurrence of two XT-isoforms in all higher organisms remains unknown and targeted genome-editing strategies could shed light on this issue. METHODS: XT-I deficient neonatal normal human dermal fibroblasts were generated by using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated proteins (Cas) 9 system. We analyzed if a reduced XT-I activity leads to abnormalities regarding ECM-composition, myofibroblast differentiation, cellular senescence and skeletal and cartilage tissue homeostasis. RESULTS: We successfully introduced compound heterozygous deletions within exon 9 of the XYLT1 gene. Beside XYLT1, we detected altered gene-expression levels of further, inter alia ECM-related, genes. Our data further reveal a dramatically reduced XT-I protein activity. Abnormal myofibroblast-differentiation was demonstrated by elevated alpha-smooth muscle actin expression on both, mRNA- and protein level. In addition, wound-healing capability was slightly delayed. Furthermore, we observed an increased cellular-senescence of knockout cells and an altered expression of target genes knowing to be involved in skeletonization. CONCLUSION: Our data show the tremendous relevance of the XT-I isoform concerning myofibroblast-differentiation and ECM-homeostasis as well as the pathophysiology of skeletal disorders.

Techniques and Algorithms for Hepatic Vessel Skeletonization in Medical Images: A Survey.

Hepatic vessel skeletonization serves as an important means of hepatic vascular analysis and vessel segmentation. This paper presents a survey of techniques and algorithms for hepatic vessel skeletonization in medical images. We summarized the latest developments and classical approaches in this field. These methods are classified into five categories according to their methodological characteristics. The overview and brief assessment of each category are provided in the corresponding chapters, respectively. We provide a comprehensive summary among the cited publications, image modalities and datasets from various aspects, which hope to reveal the pros and cons of every method, summarize its achievements and discuss the challenges and future trends.

Accuracy Assessment of Joint Angles Estimated from 2D and 3D Camera Measurements.

To automatically evaluate the ergonomics of workers, 3D skeletons are needed. Most ergonomic assessment methods, like REBA, are based on the different 3D joint angles. Thanks to the huge amount of training data, 2D skeleton detectors have become very accurate. In this work, we test three methods to calculate 3D skeletons from 2D detections: using the depth from a single RealSense range camera, triangulating the joints using multiple cameras, and combining the triangulation of multiple camera pairs. We tested the methods using recordings of a person doing different assembly tasks. We compared the resulting joint angles to the ground truth of a VICON marker-based tracking system. The resulting RMS angle error for the triangulation methods is between 12° and 16°, showing that they are accurate enough to calculate a useful ergonomic score from.

RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations.

Benefiting from the rapid development of electron microscopy imaging and deep learning technologies, an increasing number of brain image datasets with segmentation and synapse detection are published. Most of the automated segmentation methods label voxels rather than producing neuron skeletons directly. A further skeletonization step is necessary for quantitative morphological analysis. Currently, several tools are published for skeletonization as well as morphological and synaptic connectivity analysis using different computer languages and environments. Recently the Julia programming language, notable for elegant syntax and high performance, has gained rapid adoption in the scientific computing community. Here, we present a Julia package, called RealNeuralNetworks.jl, for efficient sparse skeletonization, morphological analysis, and synaptic connectivity analysis. Based on a large-scale Zebrafish segmentation dataset, we illustrate the software features by performing distributed skeletonization in Google Cloud, clustering the neurons using the NBLAST algorithm, combining morphological similarity and synaptic connectivity to study their relationship. We demonstrate that RealNeuralNetworks.jl is suitable for use in terabyte-scale electron microscopy image segmentation datasets.

Technique of vessel-skeletonized parenchyma-sparing hepatectomy for the oncological treatment of bilobar colorectal liver metastases.

BACKGROUND: To aid in the oncological management of multiple bilobar colorectal liver metastases (CRLMs), we describe a new surgical procedure, VEssel-Skeletonized PArenchyma-sparing Hepatectomy (VESPAH). STUDY DESIGN: Of 152 patients with CRLMs treated with hepatectomy, 33 patients had multiple bilobar liver metastases (≥8 liver metastases); their surgical procedures and clinical outcomes were retrospectively summarized and compared between those who underwent VESPAH and those who underwent major hepatectomy (Major Hx). RESULTS: Of the 33 patients, 20 patients were resected by VESPAH (the VESPAH group) and 13 patients by major hepatectomy (Major Hx group). The median number of CRLMs was 13 (range, 8-53) in the VESPAH group and 10 (range, 8-41) in the Major Hx group (P=0.511). No operative mortality nor severe morbidity was observed in either group. The VESPAH group showed earlier recovery of remnant liver function after surgery than the Major Hx group; the incidence of grade B/C post hepatectomy liver failure was 5% in the VESPAH group and 38% in the Major Hx group, P=0.048). Intrahepatic tumor recurrence was confirmed in 14 (70%) and 7 (54%) patients in the VESPAH and Major Hx groups, respectively (P=0.416). There was no significant difference in median overall survival (OS) after hepatectomy between the two groups; the median OS was 47 months in the VESPAH group and 33 months in the Major Hx group (P=0.481). The VESPAH group showed the higher induction rate of adjuvant chemotherapy within 2 months after surgery (P=0.002) and total number of repeat hepatectomy for intrahepatic recurrence (P=0.060) than the Major Hx group. CONCLUSIONS: VESPAH enables us to clear surgical navigation by hepatic vessel skeletonization and may enhance patient tolerability of not only adjuvant chemotherapy but also repeat hepatectomies during the patients' lifetimes.

Fractal evaluation in retinographies of individuals with different grades of diabetic retinopathy / Avaliação fractal de retinografias de indivíduos com diferentes graus de retinopatia diabética

ABSTRACT Purpose To evaluate the retinal blood vascular network of the retinographies of patients with different grades of diabetic retinopathy. Methods Ninety Retinographies (MESSIDOR database) were used, with different grades of diabetic retinopathy divided into 4 groups: no retinopathy (n=23), grade one (n=20), grade two (n=20) and grade three (n=27) diabetic retinopathy. The grades of diabetic retinopathy were classified according to the number of microaneurysms, number of hemorrhages and the presence of neovascularization. The images were skeletonized and quantified by fractal methods: dimension of box-counting (Dbc) and information (Dinf). Results The means of Dbc values of groups were around 1.25, without statistically significant difference in the dimension values between groups for whole retina. There was also no statistical difference in Dinf values between groups, whose means ranged between 1.294 ± 0.013 (group of grade 1) and 1.3 ± 0.017 (group of grade 3). The retinographies were divided into regions of equal areas. The fractal values of some retinal regions showed statistical differences, but these differences were not enough to show the sensitivity of fractal methods in identifying diabetic retinopathy. Conclusion The fractal methods were not able to identify the different grades of diabetic retinopathy in retinographies.

RESUMO Objetivo Avaliar a rede vascular sanguínea da retina a partir de retinografias de pacientes com diferentes graus de retinopatia diabética. Métodos Foram utilizadas 90 retinografias (banco de dados MESSIDOR), com diferentes graus de retinopatia diabética divididas em quatro grupos: sem retinopatia (n=23), retinopatia diabética de grau um (n=20), grau dois (n=20) e grau três (n=27). Os graus de retinopatia foram classificados conforme o número de microaneurismas, número de hemorragias e presença de neovascularização. As imagens foram esqueletizadas e quantificadas pelos métodos fractais: dimensão da contagem de caixas e informação. Resultados As médias dos valores das dimensões de contagem de caixas para todos os grupos foram próximas a 1,25, sem diferença estatisticamente significativa nos valores das dimensões entre os grupos para retina inteira. Também não houve diferença estatística nos valores da dimensão de informação entre os grupos, cujas médias variaram entre 1,294 ± 0,013 (grupo do grau 1) e 1,3 ± 0,017 (grupo do grau 3). As imagens retinianas foram divididas em regiões de áreas iguais. Os valores fractais de algumas regiões retinais mostraram diferenças estatísticas, mas estas não foram suficientes para mostrar a sensibilidade dos métodos fractais na identificação da retinopatia diabética. Conclusão Os métodos fractais não foram capazes de identificar os diferentes graus de retinopatia diabética em retinografias.

All we need to know about internal thoracic artery harvesting and preparation for myocardial revascularization: a systematic review.

Internal thoracic arteries (ITAs) are the gold standard conduits for coronary revascularization because of their long-term patency and anti-atherosclerotic properties. Harvesting and preparation of ITAs for revascularization is a technically demanding procedure with multiple challenges. Over the last few decades, various methods and techniques for ITAs harvesting have been introduced by different surgeons and applied in clinical practice with different results. Harvesting of ITAs in pedicled or skeletonized fashion, with electrocautery or harmonic scalpel, with open or intact pleura, with clipping the end or keeping it perfused; papaverine delivery with intraluminal injection, perivascular injection, injecting into endothoracic fascia, and papaverine topical spray are the different techniques introduced by the number of researchers. At the same time, access to the ITAs for harvesting has also been studied. Access and harvesting through median sternotomy, mini anterolateral thoracotomy, thoracoscopic, and robotic-assisted harvesting of ITAs are the different techniques used in clinical practice. However, the single standard method for harvesting and preparation of ITAs has yet to be determined. In this review article, we aimed to discuss and analyze all these techniques of harvesting and preparing ITAs with the help of literature to find the best way for ITAs harvesting and preparation for myocardial revascularization.

[Features of physiological groups of microorganisms - participants in the diagenesis of bone remains]. / Osobennosti fiziologicheskikh grupp mikroorganizmov ­ uchastnikov diageneza kostnykh ostankov.

Objective - to study the diversity of physiological groups of microorganisms that control the transformation of bone remains in nature. Traditional microbiological methods were used to study the cytological, physiological, biochemical and environmental properties of microorganisms isolated from the bone remains of Oryctolagus sp. 8 of 14 physiological groups of microorganisms - participants of diagenesis are established: ammonifiers, nitrifying bacteria, bacteria decomposing cellulose, causative agents of lactic acid and acetic acid fermentation, nitrogen fixators and denitrifying bacteria. Most of the identified physiological groups are in constant dynamics that is probably due to the uneven distribution in the soil of organic substances formed at different times in the process of microbial transformation of bone fragments. The analysis of qualitative and quantitative characteristics of these microorganisms' groups makes it possible not only to assess the intensity of the processes taking place over time but also to define the dependence on environmental factors such as soil acidity and ambient temperature. The results obtained can be used to obtain reliable data in forensic medical examination to solve issue about the prescription of death or the term of burial of bone remains.

Shape decomposition algorithms for laser capture microdissection.

BACKGROUND: In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous tissue samples. For the extraction to be successful, these regions have to satisfy certain constraints in size and shape and thus have to be decomposed into feasible fragments. RESULTS: We model this problem of constrained shape decomposition as the computation of optimal feasible decompositions of simple polygons. We use a skeleton-based approach and present an algorithmic framework that allows the implementation of various feasibility criteria as well as optimization goals. Motivated by our application, we consider different constraints and examine the resulting fragmentations. We evaluate our algorithm on lung tissue samples in comparison to a heuristic decomposition approach. Our method achieved a success rate of over 95% in the microdissection and tissue yield was increased by 10-30%. CONCLUSION: We present a novel approach for constrained shape decomposition by demonstrating its advantages for the application in the microdissection of tissue samples. In comparison to the previous decomposition approach, the proposed method considerably increases the amount of successfully dissected tissue.