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Nielsen FS, Pedersen MJ, Olsen MV, Larsen MS, Røge R, Jørgensen AS. Automatic Bone Marrow Cellularity Estimation in H&E Stained Whole Slide Images. Cytometry A 2019; 95:1066-1074. [PMID: 31490627 DOI: 10.1002/cyto.a.23885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/20/2019] [Accepted: 08/19/2019] [Indexed: 11/08/2022]
Abstract
Bone marrow cellularity is an important measure in diagnostic hematopathology. Currently, the gold standard for bone marrow cellularity estimation is manual inspection of hematoxylin and eosin stained whole slide images (H&E WSI) by hematopathologists. However, these assessments are subjective and subject to interobserver and intraobserver variability. This may be reduced by using a computer-assisted estimate of bone marrow cellularity. The aim of this study was to develop a fully automated algorithm to estimate bone marrow cellularity in H&E WSI stains using bone marrow segmentation. Data consisted of eight bone marrow H&E WSIs extracted from eight subjects. An algorithm was developed to estimate the bone marrow cellularity consisting of biopsy segmentation, tissue classification, and bone marrow segmentation. Segmentations of the red and yellow bone marrow (YBM) were used to estimate the bone marrow cellularity within the WSI H&E stains. The DICE coefficient between automatic tissue segmentations and ground truth segmentations conducted by an experienced hematopathologist were used for validation. Furthermore, the agreement between the automatic and two manual cellularity estimates was assessed using Bland-Altman plots and intraclass correlation coefficients (ICC). The validation of the bone marrow segmentation demonstrated an average DICE of 0.901 and 0.920 for the red and YBM, respectively. A mean cellularity estimate difference of -0.552 and - 7.816 was obtained between the automatic cellularity estimates and two manual cellularity estimates, respectively. An ICC of 0.980 (95%CI: 0.925-0.995, P-value: 5.51 × 10-7 ) was obtained between the automatic and manual cellularity estimates based on manual annotations. The study demonstrated that it was possible to obtain bone marrow cellularity estimates with a good agreement with bone marrow cellularity estimates obtained from an experienced hematopathologist. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
| | | | | | | | - Rasmus Røge
- Institute of Pathology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Metze K, Adam R, Florindo JB. The fractal dimension of chromatin - a potential molecular marker for carcinogenesis, tumor progression and prognosis. Expert Rev Mol Diagn 2019; 19:299-312. [DOI: 10.1080/14737159.2019.1597707] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Randall Adam
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - João Batista Florindo
- Department of Applied Mathematics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas, Campinas, Brazil
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Kono K, Hayata R, Murakami S, Yamamoto M, Kuroki M, Nanato K, Takahashi K, Miwa K, Tsutsumi Y, Okada K, Kaga S, Mikami T, Masauzi N. Quantitative distinction of the morphological characteristic of erythrocyte precursor cells with texture analysis using gray level co-occurrence matrix. J Clin Lab Anal 2017; 32. [PMID: 28220972 DOI: 10.1002/jcla.22175] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/18/2017] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Morphological characteristics of blood cells are still qualitatively defined. So a texture analysis (Tx) method using gray level co-occurrence matrices (GLCMs; CM-Tx method) was applied to images of erythrocyte precursor cells (EPCs) for quantitatively distinguishing four types of EPC stages: proerythroblast, basophilic erythroblast, polychromatic erythroblast, and orthochromatic erythroblast. METHODS Fifty-five images of four types of EPCs were downloaded from an atlas uploaded by the Blood Cell Morphology Standardization Subcommittee (BCMSS) of the Japanese Society of Laboratory Hematology (JSLH). Using in-house programs, two types of GLCMs-(R: d=1, θ=0°) and (U: d=1, θ=270°)-and nine types of texture distinction index (TDI) were calculated with images removed outer part of cell. RESULTS Three binary decision trees were sequentially divided among four types of EPC with the sum average of GLCM (U), the contrast of GLCM (R), and the sum average of GLCM (U). The average concordance rate (sensitivity) of CM-Tx method with the judgments of eleven experts in the BCMSS of the JSLH was 95.8% (87.5-100.0), and the average specificity was 97.6% (92.5-100.0). CONCLUSIONS The CM-Tx method is an effective tool for quantitative distinction of EPC with their morphological features.
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Affiliation(s)
- Keigo Kono
- Graduate School of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Ruka Hayata
- Department of Clinical Laboratory, KKR Sapporo Medical Center, Toyohira-ku, Sapporo, Japan
| | - Satoru Murakami
- Department of Clinical Laboratory, Japanese Red Cross Hokkaido Block Blood Center, Nishi-ku, Sapporo, Japan
| | - Mai Yamamoto
- Graduate School of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Maiko Kuroki
- Department of Health Sciences, School of Medicine, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Kana Nanato
- Department of Health Sciences, School of Medicine, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Kazuto Takahashi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan.,Department of Clinical Laboratory, Hakodate Municipal Hospital, Hakodate, Japan
| | - Keiko Miwa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan.,Department of Cardiovascular Regenerative Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yutaka Tsutsumi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan.,Department of Hematology and Oncology, Hakodate Municipal Hospital, Minato-cho, Hakodate, Japan
| | - Kazunori Okada
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Sanae Kaga
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Taisei Mikami
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Nobuo Masauzi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita-ku, Sapporo, Japan
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Immunophenotyping in myelodysplastic syndromes can add prognostic information to well-established and new clinical scores. PLoS One 2013; 8:e81048. [PMID: 24324660 PMCID: PMC3855682 DOI: 10.1371/journal.pone.0081048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/17/2013] [Indexed: 12/30/2022] Open
Abstract
Background myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic clonal disorders. So, prognostic variables are important to separate patients with a similar biology and clinical outcome. We compared the importance of risk stratification in primary MDS of IPSS and WPSS with the just described revision of IPSS (IPSS-R), and examined if variables obtained by bone marrow immunophenotyping could add prognostic information to any of the scores. Methods In this prospective study of 101 cases of primary MDS we compared the relation of patients’ overall survival with WHO types, IPSS, IPSS-R, WPSS and phenotypic abnormalities of hematopoietic precursors. We examined aberrancies in myelomonocytic precursors and CD34+ cells. Patients were censored when receiving chemotherapy or BM transplantation. Survival analysis was made by Cox regressions and stability of the models was examined by bootstrap resampling. Results median age: 64 years (15–93). WHO types: 2 cases of 5q- syndrome, 7 of RA, 64 of RCDM and 28 of RAEB. In the univariate Cox analysis, increasing risk category of all scores, degree of anemia, higher percentage of BM blasts, higher number of CD34+ cells and their myeloid fractions besides increasing number of phenotypic abnormalities detected were significantly associated with a shorter survival. In the multivariate analysis comparing the three scores, IPSS-R was the only independent risk factor. Comparing WPSS with phenotypic variables (CD34+/CD13+ cells, CD34+/CD13− cells and “total alterations”) the score and “CD34+/CD13+ cells” remained in the model. When IPSS was tested together with these phenotypic variables, only “CD34+/CD13+ cells”, and “total alterations” remained in the model. Testing IPSS-R with the phenotypic variables studied, only the score and “CD34+/CD13+ cells” entered the model. Conclusions Immunophenotypic analysis of myelomonocytic progenitors provides additional prognostic information to all clinical scores studied. IPSS-R improved risk stratification in MDS compared to the former scores.
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Matalka II, Al-Omari FA, Salama RM, Mohtaseb AH. A novel approach for quantitative assessment of mucosal damage in inflammatory bowel disease. Diagn Pathol 2013; 8:156. [PMID: 24053788 PMCID: PMC3852335 DOI: 10.1186/1746-1596-8-156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 08/26/2013] [Indexed: 12/28/2022] Open
Abstract
AIMS One of the main reliable histological features to suggest the diagnosis of inflammatory bowel disease is the presence of significant distortion of the crypt architecture indicating the chronic nature of the disease resulting in mucosal damage. This feature has a considerable intra-observer and inter-observer variability leading to significant subjectivity in colonic biopsy assessment. In this paper, we present a novel automated system to assess mucosal damage and architectural distortion in inflammatory bowel disease (IBD). METHODS The proposed system relies on advanced image understating and processing techniques to segment digitally acquired images of microscopic biopsies, then, to extract key features to quantify the crypts irregularities in shape and distribution. These features were used as inputs to an artificial intelligent classifier that, after a training phase, can carry out the assessment automatically. RESULTS The developed system was evaluated using 118 IBD biopsies. 116 out of 118 biopsies were correctly classified as compared to the consensus of three expert pathologists, achieving an overall precision of 98.31%. CONCLUSIONS An automated intelligent system to quantitatively assess inflammatory bowel disease was developed. The proposed system utilized advanced image understanding techniques together with an intelligent classifier to conduct the assessment. The developed system proved to be reliable, robust, and minimizes subjectivity and inter- and intra-observer variability. VIRTUAL SLIDES The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1797721309305023.
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Affiliation(s)
- Ismail I Matalka
- Department of Pathology and Laboratory Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Faruq A Al-Omari
- Computer Engineering Department, Hijjawi Faculty for Engineering Technology, Yarmouk University, Irbid 21163, Jordan
| | - Rola M Salama
- Department of Pathology and Laboratory Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Alia H Mohtaseb
- Department of Pathology and Laboratory Medicine, Jordan University of Science and Technology, Irbid, Jordan
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Abstract
Fractal characteristics of chromatin, revealed by light or electron microscopy, have been reported during the last 20 years. Fractal features can easily be estimated in digitalized microscopic images and are helpful for diagnosis and prognosis of neoplasias. During carcinogenesis and tumor progression, an increase of the fractal dimension (FD) of stained nuclei has been shown in intraepithelial lesions of the uterine cervix and the anus, oral squamous cell carcinomas or adenocarcinomas of the pancreas. Furthermore, an increased FD of chromatin is an unfavorable prognostic factor in squamous cell carcinomas of the oral cavity and the larynx, melanomas and multiple myelomas. High goodness-of-fit of the regression line of the FD is a favorable prognostic factor in acute leukemias and multiple myelomas. The nucleus has fractal and power-law organization in several different levels, which might in part be interrelated. Some possible relations between modifications of the chromatin organization during carcinogenesis and tumor progression and an increase of the FD of stained chromatin are suggested. Furthermore, increased complexity of the chromatin structure, loss of heterochromatin and a less-perfect self-organization of the nucleus in aggressive neoplasias are discussed.
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Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences Research Group, 'Analytical Cellular Pathology' and National Institute of Photonics Applied to Cell Biology, University of Campinas, Campinas, Brazil +55 19 32893897 kmetze.at.fcm.unicamp.br
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Shi L, Liu S, Wang D, Wong HL, Huang WH, Wang YXJ, Griffith JF, Leung PC, Ahuja AT. Computerized quantification of bone tissue and marrow in stained microscopic images. Cytometry A 2012; 81:916-21. [PMID: 22899564 DOI: 10.1002/cyto.a.22157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 01/02/2023]
Abstract
Stained histological images assist physicians to identify different types of tissues or cells and their architectures. They can be applied on the diagnosis of various diseases and the assessment of treatment effects. Osteoporosis is an aging disease that reduces the density of bones and increases the risk of bone fracture. Literatures indicate that osteoporosis is associated with the ratio of trabecular bone tissues and bone marrow cells, and bones in osteoporosis patients consist of a significantly higher marrow fat content. Interactive segmentation of bone tissue and different types of bone marrow cells in high-resolution histological images, however, is a very tedious and labor-intensive process. The aim of this study is to develop an automatic algorithm to quantify the areas of different tissues such as the trabecular bones and yellow and red marrow cells. This image segmentation method consists of a series of mathematical morphological operation steps based on both the color and morphology features of tissues and was implemented in Matlab. The results obtained from the proposed method have been verified by comparing with those obtained interactively from an experienced histotechnician (Pearson correlation coefficient > 0.94, P < 0.001). The result suggests that the proposed algorithm can effectively assist physicians to quantify stained bone histological images.
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Affiliation(s)
- Lin Shi
- Department of Imaging and Interventional Radiology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Silva DA, Basso GG, Semenzim VL, Godoy MF, Taboga SR, Andrade AL, Luvizotto MCR, Braile DM, Nery JG. Fractal dimension and Shannon's entropy analyses of the architectural complexity caused by the inflammatory reactions induced by highly crystalline poly(vinyl alcohol) microspheres implanted in subcutaneous tissues of the Wistar rats. J Biomed Mater Res A 2012; 101:326-39. [PMID: 22829297 DOI: 10.1002/jbm.a.34334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/10/2012] [Accepted: 06/26/2012] [Indexed: 12/17/2022]
Abstract
The results of the histopathological analyses after the implantation of highly crystalline PVA microspheres in subcutaneous tissues of Wistar rats are here in reported. Three different groups of PVA microparticles were systematically studied: highly crystalline, amorphous, and commercial ones. In addition to these experiments, complementary analyses of architectural complexity were performed using fractal dimension (FD), and Shannon's entropy (SE) concepts. The highly crystalline microspheres induced inflammatory reactions similar to the ones observed for the commercial ones, while the inflammatory reactions caused by the amorphous ones were less intense. Statistical analyses of the subcutaneous tissues of Wistar rats implanted with the highly crystalline microspheres resulted in FD and SE values significantly higher than the statistical parameters observed for the amorphous ones. The FD and SE parameters obtained for the subcutaneous tissues of Wistar rats implanted with crystalline and commercial microparticles were statistically similar. Briefly, the results indicated that the new highly crystalline microspheres had biocompatible behavior comparable to the commercial ones. In addition, statistical tools such as FD and SE analyses when combined with histopathological analyses can be useful tools to investigate the architectural complexity tissues caused by complex inflammatory reactions.
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Affiliation(s)
- Danilo A Silva
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
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De Mello MRB, Albuquerque DM, Pereira-Cunha FG, Albanez KB, Pagnano KBB, Costa FF, Metze K, Lorand-Metze I. Molecular characteristics and chromatin texture features in acute promyelocytic leukemia. Diagn Pathol 2012; 7:75. [PMID: 22742960 PMCID: PMC3478223 DOI: 10.1186/1746-1596-7-75] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/21/2012] [Indexed: 01/01/2023] Open
Abstract
Background Acute promyelocytic leukemia is a cytogenetically well defined entity. Nevertheless, some features observed at diagnosis are related to a worse outcome of the patients. Methods In a prospective study, we analyzed peripheral (PB) leukocyte count, immunophenotype, methylation status of CDKN2B, CDKN2A and TP73; FLT3 and NPM1 mutations besides nuclear chromatin texture characteristics of the leukemic cells. We also examined the relation of these features with patient’s outcome. Results Among 19 cases, 4 had a microgranular morphology, 7 presented PB leukocytes >10x109/l, 2 had FLT3-ITD and 3 had FLT3-TKD (all three presenting a methylated CDKN2B). NPM1 mutation was not observed. PB leukocyte count showed an inverse relation with standard deviation of gray levels, contrast, cluster prominence, and chromatin fractal dimension (FD). Cases with FLT3-ITD presented a microgranular morphology, PB leukocytosis and expression of HLA-DR, CD34 and CD11b. Concerning nuclear chromatin texture variables, these cases had a lower entropy, contrast, cluster prominence and FD, but higher local homogeneity, and R245, in keeping with more homogeneously distributed chromatin. In the univariate Cox analysis, a higher leukocyte count, FLT3-ITD mutation, microgranular morphology, methylation of CDKN2B, besides a higher local homogeneity of nuclear chromatin, a lower chromatin entropy and FD were associated to a worse outcome. All these features lost significance when the cases were stratified for FLT3-ITD mutation. Methylation status of CDNK2A and TP73 showed no relation to patient’s survival. Conclusion in APL, patients with FLT3-ITD mutation show different clinical characteristics and have blasts with a more homogeneous chromatin texture. Texture analysis demonstrated that FLTD-ITD was accompanied not only by different cytoplasmic features, but also by a change in chromatin structure in routine cytologic preparations. Yet we were not able to detect chromatin changes by nuclear texture analysis of patients with the FTLD-TKD or methylation of specific genes.
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