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1

Three dimensional visualization of histopathological data

Podwójcik Aleksandra

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2023

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Vol. 27, No 1

1--11

EN

The histopathological examination provides information about the spatial assessment of pathological changes in the tissue. The authors present a method of extending this histopathological spatial assessment with a 3D view consisting of images of microscopic layers. The proposed solution creates 3D models based on images obtained from the database of the Medical University of Gdańsk (Digital Pathology). First, a series of medical images related to the study of a specific pathological tissue undergoes a process of background detection and removal through an algorithm. Next, images aligned with each other. Then, two types of 3D models are created: 1) classical model with Marching Cubes algorithm and 2) the use Cloud of Points.

2

Accumulation of heavy metals in tilapia fish species and related histopathological changes in muscles, gills and liver of Oreochromis niloticus occurring in the area of Qahr El-Bahr, Lake Al-Manzalah, Egypt

Yacoub Amal M., Mahmoud Soaad A., Abdel-Satar Amaal M.

Oceanological and Hydrobiological Studies

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2021

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Vol. 50, No. 1

1--15

EN

Accumulation of metals (Fe, Zn, Cu, Mn, Pb, Cd and Ni) in the muscles and gills of Oreochromis niloticus, Oreochromis aureus and Tilapia zillii was assessed based on seven locations in the Qahr El-Bahr area in Lake Al-Manzalah. The average accumulation of metals was in the following order: Tilapia zillii > Oreochromis aureus > Oreochromis niloticus. To determine the risk of fish consumption, the estimated daily intake, carcinogenic, non-carcinogenic and relative risk indices were calculated. The results indicate that the intake of individual metals through the consumption of fish is almost safe for human health, whereas the intake of combined metals poses a high potential health risk to consumers. Assessment of carcinogenic risk of Cd and Ni from the consumption of tilapia species indicates that consumers are at risk of cancer. The contribution of Pb and Cd to the overall relative risk index ranged from 34% to 41%. Of the three species studied, Oreochromis niloticus is relatively safe for consumption as it poses the least health hazard, while Tilapia zillii is more predisposed to accumulate metals in its tissues. Histopathological changes were observed in the muscles, gills and liver of Oreochromis niloticus as a result of heavy metal accumulation in these organs.

3

Computational methods for automated mitosis detection in histopathology images: A review

Mathew Tojo, Kini Jyoti R., Rajan Jeny

Biocybernetics and Biomedical Engineering

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2021

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Vol. 41, no. 1

64--82

EN

Mitosis detection is an important step in pathology procedures in the context of cancer diagnosis and prognosis. Prevalent process for this task is by manually observing Hematox-ylin and Eosin (H & E) stained histopathology sections on glass slides through a microscope by trained pathologists. This conventional approach is tedious, error-prone, and has shown high inter-observer variability. With the advancement of computational technologies, automating mitosis detection by the use of image processing algorithms has attracted significant research interest. In the past decade, several methods appeared in the literature, addressing this problem and they have shown encouraging incremental progress towards a clinically usable solution. Mitosis count is an important parameter in grading of breast cancer and glioma, unlike other cancer types. Driven by the availability of multiple public datasets and open contests, most of the methods in literature address mitosis detection in breast cancer images. This paper is a comprehensive review of the methods published in the area of automated mitotic cell detection in H & E stained histopathology images of breast cancer in the last 10 years. We also discuss the current trends and future prospects of this clinically relevant task, augmenting humanity's fight against cancer.

4

HWDCNN: Multi-class recognition in breast histopathology with Haar wavelet decomposed image based convolution neural network

Kausar Tasleem, Wang MingJiang, Idrees Muhammad, Lu Yun

Biocybernetics and Biomedical Engineering

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2019

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Vol. 39, no. 4

967--982

EN

Among the predominant cancers, breast cancer is one of the main causes of cancer deaths impacting women worldwide. However, breast cancer classification is challenging due to numerous morphological and textural variations that appeared in intra-class images. Also, the direct processing of high resolution histological images is uneconomical in terms of GPU memory. In the present study, we have proposed a new approach for breast histopathological image classification that uses a deep convolution neural network (CNN) with wavelet decomposed images. The original microscopic image patches of 2048 1536 3 pixels are decomposed into 512 384 3 using 2-level Haar wavelet and subsequently used in proposed CNN model. The image decomposition step considerably reduces convolution time in deep CNNs and computational resources, without any performance downgrade. The CNN model extracts the deep features from Haar wavelet decomposed images and incorporates multi-scale discriminant features for precise prognostication of class labels. This paper also solves the demand for massive histopathology dataset by means of transfer learning and data augmentation techniques. The efficacy of proposed approach is corroborated on two publicly available breast histology datasets-(a) one provided as a part of international conference on image analysis and recognition (ICIAR 2018) grand challenge and (b) on BreakHis data. On the ICIAR 2018 validation data, our model showed an accuracy of 98.2% for both 4-class and 2-class recognition. Further, on hidden test data of the ICIAR 2018, we achieved an accuracy of 91%, outperforming existing state-of-the-art results significantly. Besides, on BreakHis dataset, the model achieved competing performance with 96.85% multi-class accuracy.

5

Automatic segmentation of cell nuclei using Krill Herd optimization based multi-thresholding and Localized Active Contour Model

Beevi K. S., Nair M. S., Bindu G. R.

Biocybernetics and Biomedical Engineering

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2016

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Vol. 36, no. 4

584--596

EN

Analysis of tissue components in histopathology image stays on as the gold standard in detecting different types of cancers. Active Contour Models (ACM) serve as a widely useful tool in object segmentation in pathology images. Since the ACMs are susceptible to initial contour placement, efficiency of object detection is very much influenced by the selection of primary curve placement technique. In this paper, in order to handle diffused intensities present along object boundaries in histopathology images, segmentation of nuclei from breast histopathology images are carried out by Localized Active Contour Model (LACM) utilizing bio-inspired optimization techniques in the detection stage. Krill Herd Algorithm (KHA) based optimal curve placement provides better initial boundaries compared with other detection techniques. The segmentation performance is investigated based on Housdorff (HD) and Maximum Absolute Distance (MAD) measures. The algorithm also shows comparable performance with other state-of-the-art techniques in terms of quantitative measures such as Precision, Accuracy and Touching Nuclei Resolution when applied to complex images of stained breast biopsy slides.

6

Heavy metal content and histopathology of the tissues of the yellow-necked mice(Apodemus flavicollis) and bank voles (Clethrionomys glareolus) as an exposure indicato of environmental pollution in Małopolska province

Gdula-Argasińska J., Dąbrowski Z., Witkowska-Pelc E., Sawicka-Kapusta K.

Chemia i Inżynieria Ekologiczna

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2005

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Vol. 12, nr 11

1213-1220

EN

Yellow-necked mice (Apodemus flavicollis, Melchior 1834) and bank voles (Clethrionomys glareolus, Schreber 1780) were trapped in eight forest sites of Małopolska province. Heavy metals (cadmium, lead) content were analyzed in livers and kidneys of rodents. Also Some histopathology of liver and kidney tissues were investigated. It was shown from the analysis that high metals concentrations were detected in animals from Ojcowski Natinal Park, Olkusz Porest, Bonarka, Rajsko and Wola Rzędzińsk,a - sites under anthropopressure. Many histopathological changes were found in tissues of mice and voles from Olkusz Porest and from Ojców NP, and also heavy metals concentrations were high in tissues of animals from these-sites. Mice and voles from the agglomeration sites accumulated high level of metals. This project allowed to assessing physiological condition of mammals from medium and strongly polluted areas. Prom the data it was observed that rodents with the short life-span so with the short time of exposure had worse physiological condition which may be caused by contaminants.

PL

Przedmiotem badań była ocena wpływu metali ciężkich na organizmy myszy leśnych (Apodemus flavicollis, Melchior 1834) i nornic rudych (Clethrionomys glareolus, Schreber 1780) odłowionych w wybranych ekosystemach leśnych Małopolski o różnym stopniu zanieczyszczenia. Analizowano poziom metali ciężkich (kadmu i ołowiu) w wątrobach i nerkach odłowionych gryzoni, wykonano również analizy histologiczne. Analizując rezultaty, stwierdzono, że najwyższe poziomy metali ciężkich zakumulowały gryzonie odłowione w Ojcowskim PN, lasach olkuskich, Bonarce, Rajsku i w Woli Rzędzińskiej - miejscach pozostających pod wpływem antropopresji. U myszy leśnych i nornic rudych pozyskanych w Ojcowskim PN i w lasach olkuskich wykazano zmiany histopatologiczne wątrób i nerek, jak również najwyższe koncentracje kadmu i ołowiu w tych narządach. Zwierzęta pochodzące z terenów przemysłowych charakteryzowały się większą akumulacją metali w poszczególnych tkankach i zmianami histopatologicznymi wątroby i nerek w porównaniu ze zwierzętami z terenów mniej zanieczyszczonych. Można stwierdzić, że gryzonie, charakteryzujące się krótkim okresem życia, a więc również krótkim okresem ekspozycji, wykazują zdecydowanie gorszą kondycję fizjologiczną. Świadczy to o niekorzystnych warunkach ich życia, nawet w średnio zanieczyszczonych terenach.

7

Cadmium and lead concentrations and histopathological analysis of tissues of rodents from within the neighbourhood of steelworks and zinc smelters

Damek-Poprawa M., Dąbrowski Z., Sawicka-Kapusta K.

Chemia i Inżynieria Ekologiczna

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2002

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Vol. 9, nr 10

1193--1198

EN

Bank voles Clethrionomys glareolus and yellow-necked mice Apodemus flavicollis were caught and taken from the neighbourhood of the Lucchini Steelworks in Warsaw and the Sendzimir Steelworks in Krakow. Rodents were also caught near two zinc works in the Upper Silesia region, namely in Bukowno and Miasteczko Slaskie. Borecka forest in the north of Poland was chosen as the control area. Pb and Cd concentrations in the liver, kidneys, femurs and testes were determined. The statistically significantly highest concentration of lead (173 µg ּ g-1) was found in the femurs of the yellow-necked mice from Bukowno. The highest concentrations of cadmium were found in the kidneys of the bank voles and of the yellow-necked mice also from Bukowno: there were 33 µg Cd ּ g-1 and 23,6 µg Cd ּ g-1 respectively. Iron, copper and zine levels in tissues were also analysed, but their concentrations did not exceed the established critical values. Histomorphological changes were examined in the livers and kidneys of rodents trapped in the areas surrounding steelworks and zine smelters. The tissues of rodents from the control area showed no damage.

PL

W sąsiedztwie dwóch hut stali: Huty im. T. Sendzimira w Krakowie i Huty Lucchini – Warszawa w Warszawie oraz dwóch hut cynku: w Bukowinie i w Miasteczku Śląskim przeprowadzono odłowy nornic rudych Clethrionomys glareolus i myszy leśnych Apodemus flavicollis. Puszcza Borecka wybrana została jako teren kontrolny. Zbadano poziomy ołowiu, kadmu, żelaza, cynku i miedzi wątrobach, nerkach, kościach i jądrach odłowionych zwierząt. Statystycznie istotnie najwyższe stężenie ołowiu (173 µg ּ g-1) odnotowano w kościach myszy leśnych z Bukowna. Najwyższe koncentracje kadmu stwierdzono w nerkach nornic rudych (33 µg ּ g-1) i myszy leśnych (23,6 µg ּ g-1) również z okolic Bukowna. Podlegające homeostatycznej regulacji poziomy pierwiastków fizjologicznych (Fe, Zn, Cu) nie przekroczyły wartości krytycznych. Przeanalizowano zmiany histopatologiczne powstałe pod wpływem ołowiu i kadmu w wątrobach i nerkach gryzoni odłowionych w sąsiedztwie hut stali i hut cynku. W tkankach zwierząt pochodzących z terenu kontrolnego nie stwierdzono żadnych uszkodzeń.

8

Histologiczna ocena kompozytu węgiel-żywica epoksydowa w oparciu o badania doświadczalne na zwierzętach

Bajor G., Sabat D., Szczurek Z.

Inżynieria Biomateriałów

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2000

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R. 3, nr 12

3--7

PL

Dla celów realizacji tego eksperymentu użyto królików, którym wszczepiano do światła jamy szpikowej kości udowej grot z kompozytu węgiel - żywica epoksydowa. Kompozyt ten charakteryzuje się bardzo dobrymi właściwościami mechanicznymi, co między innymi ułatwia obróbkę mechaniczna, umożliwia otrzymywanie implantów o złożonych kształtach. Do eksperymentu użyto sześć królików z zastosowaniem kompozytu włókno węglowe, osnowa epoksydowa pokrytych warstwą hydroksyapatytu /implant C-ep-HAP / w okresach obserwacji 4, 14, 18, 20, 22 tygodni. Celem przeprowadzonego badania było określenie przydatności tego materiału jako elementu zespalającego kość, oraz jego biozgodności. Wykazano, że w szpiku kostnym otaczającym grot zachodzą procesy resorpcji, a następnie odbudowy kości aż do powstania dojrzałej kości gąbczastej. Tym przemianom towarzyszyła postępująca biodegradacja fragmentów wszczepu, aż do powstania zbrylonych struktur i ich pyłowego rozpadu. Fragmenty tego materiału działają stymulująco na odnowę kości gąbczastej i nie wywoływały odczynu olbrzymiokomórkowego ani zmian bliznowatych. W oparciu o przeprowadzone badania potwierdzono walory wytrzymałościowe tego materiału oraz jego biozgodność. Natomiast uzyskano jedynie potwierdzenie powolnej biodegradacji rozpoczynającej się na powierzchni tego materiału.

EN

Rabbits with the arrow head-shaped carbon-epoxy resin composite implanted into the femoral bone marrow cavity were used in the experiment. The composite has very good mechanical properties, which enable mechanical working and formation of complex shapes. Six rabbits with implants made of carbon fibre - epoxy resin composite, coated with hydroxyapatite / C-ep-HAP implant/, were used in 4, 14, 18, 20, 22 weeks of observation. The aim of the experiment was to determine the usefulness of the composite material as an element uniting bones as well as its biocompatibility. It has been shown that in the bone marrow surrounding the implant there take place the processes of resorption and bone restoration leading to the formation of a mature spongy bone. These changes are accompanied by progressive biodegradation of the implanted fragments, i.e. lumping and dusting. Fragments of the implanted material stimulate restoration of spongy bone and do not cause gigantocellular reaction or cicatricial changes. The investigations carried out in this work confirmed good strength and biocompatibility of the implant material. Only slow biodegradation beginning on the surface of the material was observed.

9

Biotolerancja implantów ze stali AlSl 316L z warstwami pasywnymi i pasywno-diamentowymi

Koczy B., Marciniak J.

Inżynieria Biomateriałów

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2000

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R. 3, nr 11

23--31

PL

Przedstawiono wyniki badań biotolerancji implantów metalicznych ze stali AlSl 316L uszlachetnionych warstwami pasywnymi i pasywno - diamentowymi w doświadczeniach na modelach zwierzęcych jakim były świnki morskie. Badania miały na celu wykazanie przydatności tego materiału dla chirurgii urazowo - ortopedycznej i szczękowo - twarzowej. Doświadczenia przeprowadzono według zaleceń normy ASTM 981-86. Implanty wszczepiono do tkanek podskórnych, mięśniowych i kostnych zwierząt. Obserwacje histopatologiczne tkanek zwierząt grupy kontrolnej i doświadczalnej prowadzono po okresach 12, 26 i 52 tygodni. Oprócz badań tkanek okołowszczepowych prowadzono także badania histopatologiczne tkanek miąższowych organów detoksykacyjnych. Na podstawie przeprowadzonych badań można stwierdzić, że warstwy pasywne i pasywno - diamentowe, wytworzone sposobem opracowanym w Zakładzie Materiałów Biomedycznych Politechniki Śląskiej oraz Zakładzie Materiałów Cienkowarstwowych Politechniki Łódzkiej cechują dobre właściwości zaporowe. Blokują skutecznie inicjację i rozwój korozji implantów, a w konsekwencji infiltrację jonów metalicznych do tkanek. Uzyskane wyniki są więc obiecujące do zastosowań wymienionych biomateriałów metalicznych dla praktyki klinicznej w chirurgii rekonstrukcyjnej, a w szczególności urazowo-ortopedycznej oraz szczękowo-twarzowej.

EN

Results of biotolerance investigations ace presented of the metallic implants from fhe AlSl 316L steel improved with the passive and passive-diamond coatings in experioments on the animal models fea tured by guinea -pigs. The purpose was to demonstrate their applicability in the traumatic-orthopaedic and maxillofacial surgery. The experiments were carried out according to the ASTM 981-86 standard. The implants were inserted into the subcutaneous, muscular, and osseous tissues of the animals. Histopathological observations of tissues of the animals from the control and experimental groups were carried out after 12, 26 and 52 weeks. Apart from examination of the peri-implant tissues, the histopathological examinations were also made of the parenchymatous tissues of the detoxication organs. Basing on these experiments, one can state that the passive and passive-diamond coatings deposited according to the method development in the Division of Biomedical Materials Engineering of the Silesian University of Technology and in the Division of Thin-Layer Materials of the Technical University of Łódź have good barrier properties. They effectively block the initiation and development of the implant corrosion, and in consequence, infiltration of rnetal ions into the tissues. The obtained results are thus promising for application of the aforementioned metallic biomaterials in the clinical practice for the reconstructive surgery, and particularly for the traumatic-orthopaedic and maxillofacial surgery.

10

Extending DIPS software package for research and routine investigations of biomedical images

Piętka D., Dulewicz A., Jaszczak P., Nechay A.

Machine Graphics and Vision

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1998

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Vol. 7, No. 4

711-723

EN

The paper introduces DIPS (Digital Images Procesing System), a new, original software package, developed to meet specific requirements of image analysis in scientific environment. Without gooing deeply into programming details, key features of the system are highlighted: flexibility when designing new picture processing schemes and simplicity when performing routine tasks.