Sürdürülebilir Kalkınma Amaçları
Yayınlar
- BildiriAçık Erişim2024High-Accuracy Hand Segmentation for Palmprint Biometric Systems Improving Auto-Encoder Techniques
Yalcin, Kadir; Dogan, Ramazan Ozgur; Dogan, Hulya; Bingol, Ozkan
Biometric technologies have been widely adopted in various commercial products, ranging from security systems to personal devices, due to their exceptional reliability and user-friendliness. Among these, palmprint biometrics has gained increasing attention for its advantages, such as ease of use, a larger surface area, and the ability to capture more features compared to other biometric methods. A typical palmprint biometric system involves five key stages: (a) Image Acquisition, (b) Hand Segmentation, (c) Pattern Generation, (d) Feature Extraction, and (e) Verification/Identification. The overall success of the system depends on the effectiveness of each stage, with hand segmentation being crucial for identifying the most relevant features for accurate verification. This study aims to achieve high-accuracy biometric recognition by segmenting hands from images captured in uncontrolled environments with complex backgrounds. Accuracy (ACC), Intersection over Union (IoU), F1-Score, and Dice Coefficient are the four critical metrics used to assess the performance of segmentation techniques. The findings demonstrate that the U-Net + ViT and MA-Net + ResNet34 techniques outperform traditional auto-encoder methods in both quantitative performance metrics and visual analysis, leading to significantly improved hand segmentation for biometric systems.
- MakaleAçık Erişim2024DL-EDOF: Novel Multi-Focus Image Data Set and Deep Learning-Based Approach for More Accurate and Specimen-Free Extended Depth of Focus
Dogan, Hulya; Dogan, Ramazan Ozgur; Ay, Ilyas; Sezen, Sena F.
Depth of focus (DOF) is defined as the axial range in which the specimen stage moves without losing focus while the imaging apparatus remains stable. It may not be possible to capture an image that includes the entire specimen in focus due to the narrow DOF in microscopic systems. Extended depth of focus (EDOF) is used to overcome this limitation in microscopic systems. Although the researchers have developed so many EDOF microscope approaches, this research field still has some crucial shortcomings such as high computational costs, complexity and execution time, requiring additional equipment, low precise characterization of curves, and edges in images, varying performance depending on the specimen and microscope, using only gray levels of input images to acquire the pixel’s focus values. In order to minimize these shortcomings and comprehensively analyze the performance of EDOF approaches, a novel multi-focus image data set is generated, and a deep learning-based EDOF microscope approach is proposed in this study. When compared with the state-of-art EDOF approaches, our study provides various crucial contributions such as the first EDOF approach based on unsupervised deep learning, providing more accurate and specimen-free EDOF, generating a novel multi-focus image data, not requiring any pre- or post-processing technique and acquiring the pixel’s focus degrees using deep features. In order to evaluate the effectiveness of the suggested approach, 20 different EDOF approaches are applied to a multi-focus image data set containing 9 image collections (4 synthetic and 5 microscope image collections) in total. Performance analysis metrics with and without requiring a reference image are preferred to identify which EDOF microscope approach can extract more essential details from the multi-focus images for the synthetic and microscope image collections, which are Root Mean Square Error (RMSE), Peak Signal Noise Ratio (PSNR), Universal Quality Index (UQI), Correlation Coefficient (CC), Perception-based Image Quality Evaluator (PIQE), Blind/Referenceless Image Spatial Quality Evaluator (BRISQUE), Extension of Universal Quality Index for N Images (UQIN), and Naturalness Image Quality Evaluator (NIQE). Objective and subjective analysis of this study demonstrates that unsupervised deep learning model is more efficient to transmit crucial details from multi-focus images. Moreover, the suggested EDOF microscope approach with highest PSNR, UQI, CC, UQIN and lowest RMSE, PIQE, BRISQUE, NIQE produces higher performance than the state-of-art approaches.
- BildiriAçık Erişim2024An Efficient Technique Based on Deep Learning for Automatic Focusing in Microscopic System
Dogu, Fatma Tuana; Dogan, Hulya; Dogan, Ramazan Ozgur; Ay, Ilyas; Sezen, Sena F.; Seyman, M.
During microscopic examination process, experts firstly determine the most appropriate focusing point by precisely moving the microscope stage in the Z axis. This manual focusing process may cause variability in results depending on hand-eye coordination and individual experience. Therefore, the development of automatic focusing offers superior quality and consistent imaging. Many researchers have studied automatic focusing systems and proposed many focus functions to extract focus information from multi-focus images. Nevertheless, these focusing systems still consist of several significant limitations such as requiring a supplementary material, longer running time, producing different performance depending on the sample and magnification objective. In this study, an efficient technique based on deep learning is proposed to automatically determine the focused image during microscopic examination processes to minimize these limitations in the literature. This technique takes a sequence of images with the same field of view and different focuses as input and gives the image with maximum focusing as output. The proposed technique is compared with other automatic focusing techniques on the literature. In this study, novel multi-focus image sequences obtained from liver, intestine, heart, kidney, and lung samples is prepared to evaluate the performance of automatic focusing techniques. These sequences are obtained by scanning with 10× and 40× magnification objectives. Running time, accuracy, number of local maximum points, range, and noise levels are used as evaluation criteria in this study. According to evaluation criteria results obtained in this study, it has been proven that the proposed technique provides better performance than other automatic focusing techniques.
- MakaleAçık Erişim2023Floresan Mikroskop Sistemlerinde Yüksek Doğruluklu Nükleer Segmentasyonu için Otomatik Kodlayıcı Tabanlı Modellerin Geliştirilmesi
Doğan, Ramazan Özgür; Dogan, Hulya; Emir, Sümeyye Nur; Danışmaz, Sibel
Mikroskobik sistemlerde doku veya hücre numunelerinde nükleer morfoloji veya biyolojik belirteçler gibi bölümleri görselleştirmek için hematoksilen ve eozin (Hematoxylin and eosin - H&E) histolojik boyamalar, immünohistokimyasal (immunohistovhemical - IHC) ve immünofloresan (immunofluorescence - IF) boyama yaklaşımları geliştirilmiştir. H&E veya IHC boyamalar ile karşılaştırıldığında, IF boyamaların sayısala aktarılması uzmanlar için daha zorlu ve zaman alıcı olmaktadır. Fakat, IF boyama yaklaşımlarında daha fazla hücresel veya hücre altı belirteç görüntülenebilmektedir. Floresan mikroskoplardan elde edilmiş nükleer segmentasyonunun yüksek doğrulukla otomatik gerçekleştirilmesi IF boyama yaklaşımlarındaki hücreler hakkında daha fazla bilgi elde edilmesini sağlamaktadır. Literatürde diğer mikroskobik sistemlerden elde edilmiş görüntülerde hücre veya doku segmentasyonu için birçok çalışma geliştirilmiş ve yüksek doğruluklu sonuçlar elde edilmiştir. Fakat diğer alanlarda gerçekleştirilen bu başarı, floresan mikroskoplardan elde edilmiş görüntülerdeki nükleer segmentasyonu için elde edilmemiştir. Bu kapsamda, çalışmada floresan mikroskop sistemlerinde nükleer segmentasyonu için yüksek doğruluklu otomatik kodlayıcı modelleri geliştirilmektedir. Geliştirilen otomatik kodlayıcı modellerinin analizi uzman kişiler tarafından işaretlenmiş, floresan mikroskop görüntülerinden oluşan veri seti kullanılarak gerçekleştirilmektedir. Çalışmada kullanılan performans değerlendirme prosedürleri açısından, gerçekleştirilen otomatik kodlayıcı modellerinin başarılarının otomatik nükleer segmentasyon için tatmin edici olduğu açıkça görülmektedir.
- MakaleAçık Erişim2023Odaklama derinliğinin artırılmasında derin özelliklerin odaklama değerlerinin çıkarılmasındaki etkilerinin incelenmesi
Doğan, Ramazan Özgür; Dogan, Hulya; Emir, Sümeyye Nur; Danışmaz, Sibel
Mikroskobik sistemlerde var olan odaklama derinliğinden dolayı numunenin tüm alanının odaklandığı görüntü elde etmek imkânsız olabilmektedir. Bu durum, mikroskobik sistemlerde görüntü işleme ve yapay zekâ algoritmaları kullanılarak gerçekleştirilen sınıflandırma, bölütleme, hizalama (registration), panoramik birleştirme (stitching) gibi uygulamalarının başarılarını olumsuz yönde etkilemektedir. Literatürde numunenin tüm alanının odaklandığı görüntü elde etmek için odaklama derinliğinin artırılması yaklaşımları geliştirilmektedir. Literatür çalışmaları, bu yaklaşımların, görüntülerdeki eğrilerin ve kenarların düşük kesinlikte karakterizasyonu, daha yüksek koşma süresi ve incelenen numuneye ve kullanılan mikroskoba göre performans değişimi gibi çeşitli kısıtlamalara sahip olduklarını ortaya koymaktadır. Ek olarak, bu yaklaşımlar odaklama bilgilerini genelde görüntülerin gri seviye değerlerini kullanarak hesaplamaktadırlar. Bu çalışmada bu kısıtlamaları minimize etmek için yeni bir odaklama derinliğinin artırılması yaklaşımı geliştirilmekte ve odaklama derinliğinin artırılmasında derin özelliklerin odaklama değerlerinin çıkarılmasındaki etkileri incelenmektedir. Çalışmada elde edilen sonuçlar derin özelliklerin piksellerin odaklama değerlerini hesaplamada gri seviye değerlerine göre daha etkin olduğunu göstermektedir.
- MakaleYalnız künye2023İlaç - İlaç Etkileşimi Tahmini için Konvolüsyonel Sinir Ağı Tabanlı Yeni Bir Yaklaşım
Doğan, Ramazan Özgür; Sezen, Feride Sena; Dogan, Hulya
Aynı anda birden fazla ilaç kullanımında özellikle son yıllarda büyük artış görülmektedir. Bu durum ilaçlar arası reaksiyon olarak tanımlanan ilaç – ilaç etkileşimlerine yol açabilmektedir. Hastalarda oluşabilecek olumsuz durumların engellenmesi için ilaçlar arasındaki etkileşimlerin tahmin edilmesi gerekmektedir. İlaç – ilaç etkileşimlerinin tahmini genelde deneyler ile gerçekleştirmekte ve yoğun iş yükü gerektirmektedir. Klinisyenlerin daha doğru kararlar alması ve uygun tedavi programları oluşturması için literatürde otomatik ilaç – ilaç etkileşimi tahmini gerçekleştiren yaklaşımlar sıklıkla gerçekleştirilmiştir. Literatürde ilaç – ilaç etkileşimi tahmini için birçok çalışma geliştirilmesine rağmen, bu alanda hala belirgin kısıtlamalar mevcuttur. İlaç – ilaç etkileşimi tahmini alanında karşılaşılan kısıtlamaları minimize etmek amacıyla bu çalışmada ilaçların yapısal özellikleri kullanılarak literatürdeki çalışmalardan daha gelişmiş konvolüsyon sinir ağı modeli önerilmektedir. Önerilen yaklaşım, özellik çıkarma ve konvolüsyon sinir ağı modelinin tasarımı olmak üzere iki ana aşamada gerçekleştirilmektedir. Çalışmada kullanılan performans değerlendirme prosedürleri açısından, önerilen yaklaşımın başarısının ilaç – ilaç etkileşimi tahmini için tatmin edici olduğu açıkça görülmektedir.
- MakaleAçık Erişim20233B Şekil Oluşturmak için Alt Örneklemesiz Shearlet Dönüşümüne Dayalı Yeni ve Yüksek Kaliteli Odaklama Ölçüm Operatörü
Doğan, Ramazan Özgür; Dogan, Hulya
3B şekil oluşturulma sürecinde herhangi ek donanım gerektirmeyen Odaktan Şekil (Shape From Focus - SFF) en çok tercih edilen stratejilerdendir. SFF stratejisi, 3B şekil oluşturma sürecinde farklı odaklı 2B görüntü serisi kullanmakta ve üç temel aşamadan oluşmaktadır: (1) Farklı odaklı 2B görüntü serisinin elde edilmesi, (2) Görüntü piksellerinin odaklama değerlerinin hesaplanması ve (3) Maksimum odaklı pikselin seçilmesi. Yüksek doğruluk ve daha düşük gürültü ile 3B şekil oluşturmak için, araştırmacılar SFF'nin ikinci aşamasında yeni odaklama ölçüm operatörü önermek yerine genellikle bir ön veya son işlem algoritmaları geliştirmektedirler. Literatür çalışmalarının aksine, bu çalışmada herhangi bir ön veya son işlem gerektirmeyen Alt Örneklemesiz Shearlet Dönüşümü'ne dayalı yeni ve yüksek kaliteli odaklama ölçüm operatörü önerilmektedir. Önerilen odaklama ölçüm operatörünün etkinliği sentetik görüntü serileri kullanılarak pencere boyutu ve gürültü seviyesi gibi farklı koşullar altında analiz edilmektedir. Elde edilen öznel ve nesnel sonuçlar önerilen odaklama ölçüm operatörünün daha iyi performans sağladığını göstermektedir.
- BildiriYalnız künye2023Deep Learning Based Focus Measurement Operator for 3D Imaging in Microscopic Systems
Dogan, Hulya; Dogan, Ramazan Ozgur
Since 3D imaging in microscopic systems makes cell and tissue structures more prominent and visible, it provides higher performance in image processing applications such as automatic segmentation, recognition, classification, alignment and stitching. For this reason, 3D imaging in microscopic systems has been one of the most comprehensive and long-studied research areas in the literature. It seems that the most frequently preferred strategy for 3D imaging is shape from focus. Shape from focus is a strategy that uses a sequence of 2D images with the same perspective and different focused regions to create the 3D shape of the sample. Focus measurement operators are applied to extract the focus properties of the input images in shape from focus strategies. These operators have several limitations, such as more precise characterization of curves and edges in images. Researchers often use a pre- or post-processing technique to minimize these limitations, rather than proposing a new focus measurement operator. In this study, a deep learning based focus measurement operator, which does not require a pre- or post-processing technique, is developed to eliminate these limitations. The qualitative and quantitative results obtained in the study show that the proposed focus measurement operator is more effective in 3D imaging than other operators in the literature.
- BildiriYalnız künye2023An Extensive Study: Creation of A New Inverted Microscope Image Data Set and Improving Auto-Encoder Models for Higher Accuracy Segmentation of HaCaT Cell Culture Line
Sevim, Zeynep; Dogan, Hulya; Demir, Zeynep; Sezen, Feride Sena; Dogan, Ramazan Ozgur
In cell culture investigations, it is assumed that the number of cells is counted automatically without the need for forward planning, additional tools, or consumables. The automatic cell counting process is greatly facilitated and made functional by the segmentation of cell culture lines. Many studies with high-accuracy results have been developed for cell or tissue segmentation in images acquired from microscopic systems, but this success cannot be achieved for segmentation of cell culture line (especially in images acquired from inverted microscope). There are still restrictions in segmentation of cell culture line studies in inverted microscope systems. In this context, a new inverted microscope image data set is created and higher accuracy auto-encoder models are developed for segmentation of HaCat cell culture line. The analyzes of the developed auto-encoder models are evaluated using four different performance evaluation procedures which are Accuracy, Sensitivity, Specificity and Jaccard. In terms of the performance evaluation procedures used in this study, the achievements of the auto-encoder models are clearly satisfactory for the automated segmentation of the HaCat cell culture line.
- BildiriYalnız künye2023An Efficient 1D Autoencoder-Based Approach for R-Peaks Detection in Electrocardiogram Signals
Dogan, Ramazan Ozgur; Dogan, Hulya; Kayikcioglu, Temel
Electrocardiogram (ECG) signal which is composition of multiple segments such as P-wave, QRS complex and T-wave plays a crucial role in evaluating human heart cardiac diagnosis. For an analysis of cardiac diagnosis, it is required that clinicians scan the ECG signal for R-peaks (the highest peak of the QRS complex) detection, which relies on their expertise and takes enormous time. In order to provide more realistic treatment of cardiovascular diseases in the ECG signal with noises and different characteristics, computer-based R-peaks detection approaches have been actively developed in the research article for many years and generally compose of two major operations; preprocessing and decision. Contrary to previous approaches which require high computational costs and complexity, appropriate initial parameters, a novel CNN based approach is presented for R-peaks detection in this paper. Both qualitative and quantitative analysis are performed in the real ECG signal taken from typical MIT-BIH arrhythmia database. In order to validate the success of the recommended approach, total 18 different R-peaks detection approaches reported in the literature are compared by utilizing performance evaluation metrics. Average values of sensitivity, positive predictivity, error rate, accuracy and f-score are computed as 99,96%, 99,95%, 0,09%, 99,90% and 99,95% respectively, which are the best values among well-established studies for R-peaks detection. It is demonstrated with qualitative and quantitative results that better performance is achieved by our suggested approach.
- Derleme MakaleYalnız künye2023A Comprehensive Review of Computer-based Techniques for R-Peaks/QRS Complex Detection in ECG Signal
Dogan, Hulya; Dogan, Ramazan Ozgur
Electrocardiogram (ECG) signal, which is composite of multiple segments such as P-wave, QRS complex and T-wave, plays a crucial role in the treatment of cardiovascular disease. For an analysis of cardiac diagnosis, it is required that clinicians scan the ECG signal for QRS complex or R-peaks (the highest peak of the QRS complex) detection, which relies on their expertise and takes enormous time. In order to provide more realistic treatment of cardiovascular diseases, so many computer-based techniques detecting R-peaks/QRS complex in the ECG signal with noises and different characteristics have been actively developed in research article for many years. Moreover, researchers have created various data sets for R-peaks/QRS complex detection. Although R-peaks/QRS complex detection is one of the notable research areas with so many computer-based techniques and ECG data sets, no comprehensive review paper have been published recently. The main aim of this study is to present a wide range of computer-based techniques proposed for detection of R-peaks/QRS complex. First of all, in this study, computer-based techniques proposed in the literature for the detection of R-peaks/QRS complex and their stages are introduced in detail. The generalization ability of these techniques is investigated deeply. Details are given about the most preferred ECG data sets produced in the literature for the analysis of computer-based techniques. Finally, the performances of computer-based techniques and generalization abilities are analyzed for each data set created in the literature by giving the results of the evaluation metrics.
- MakaleAçık Erişim2021A Two-Phase Approach using Mask R-CNN and 3D U-Net for High-Accuracy Automatic Segmentation of Pancreas in CT Imaging
Dogan, Ramazan Ozgur; Dogan, Hulya; Bayrak, Coskun; Kayikcioglu, Temel
Background and objective: The size, shape, and position of the pancreas are affected by the patient characteristics such as age, sex, adiposity. Owing to more complex anatomical structures (size, shape, and position) of the pancreas, specialists have some difficulties in the analysis of pancreatic diseases (diabetes, pancreatic cancer, pancreatitis). Therefore, the treatment of the disease requires enormous time and depends on the experience of specialists. In order to decrease the rate of pancreatic disease deaths and to assist the specialist in the analysis of pancreatic diseases, automatic pancreas segmentation techniques have been actively developed in the research article for many years. Methods: Although the rapid growth of deep learning and proving satisfactory performance in many medical image processing and computer vision applications, the maximum Dice Similarity Coefficients (DSC) value of these techniques related to automatic pancreas segmentation is only around 85% due to complex structure of the pancreas and other factors. Contrary to previous techniques which are required significantly higher computational power and memory, this paper suggests a novel two-phase approach for high-accuracy automatic pancreas segmentation in computed tomography (CT) imaging. The proposed approach consists of two phases; (1) Pancreas Localization, where the rough pancreas position is detected on the 2D CT slice by adopting Mask R-CNN model, (2) Pancreas Segmentation, where the segmented pancreas region is produced by refining the candidate pancreas region with 3D U-Net on the 2D sub-CT slices generated in the first phase. Both qualitative and quantitative assessments of the proposed approach are performed on the NIH data set. Results: In order to evaluate the achievement of the recommended approach, a total of 16 different automatic pancreas segmentation techniques reported in the literature are compared by utilizing performance assessment procedures which are Dice Similarity Coefficient (DSC), Jaccard Index (JI), Precision (PRE), Recall (REC), Pixel Accuracy (ACC), Specificity (SPE), Receiver Operating Characteristics (ROC) and Area under ROC curve (AUC). The average values of DSC, JI, REC and ACC are computed as 86.15%, 75.93%, 86.27%, 86.27% and 99.95% respectively, which are the best values among well-established studies for automatic pancreas segmentation. Conclusion: It is demonstrated with qualitative and quantitative results that our suggested two-phase approach creates more favorable results than other existing approaches.
- BildiriYalnız künye2015Virtual Mouse Control with Hand Gesture Information Extraction and Tracking
Dogan, Ramazan Ozgur; Dogan, Hulya; Köse, Cemal
Virtual mouse implemented with hand gesture tracking based on image is one of studies in human-computer interaction. In this study that human-computer interaction is implemented with virtual mouse is purposed. This study consists of three main steps that are hand gesture tracking, features of hand region extraction and classification of these features. In this study hand gesture tracking is generated with Camshift (Continuously Adaptive Mean Shift) algorithm, features of hand gestures are extracted with bag of visual words and these features are classified with support vector machines. Detailed tests are performed to compare success of tracking, features extraction and classisfication methods and that this system works successfully is shown.