A Generic Fundus Image Enhancement Network Boosted by Frequency Self-supervised Representation Learning

Fundus photography is prone to suffer from image quality degradation that impacts clinical examination performed by ophthalmologists or intelligent systems. Though enhancement algorithms have been developed to promote fundus observation on degraded images, high data demands and limited applicability hinder their clinical deployment. To circumvent this bottleneck, a generic fundus image enhancement network (GFE-Net) is developed in this study to robustly correct unknown fundus images without supervised or extra data. Levering image frequency information, self-supervised representation learning is conducted to learn robust structure-aware representations from degraded images. Then with a seamless architecture that couples representation learning and image enhancement, GFE-Net can accurately correct fundus images and meanwhile preserve retinal structures. Comprehensive experiments are implemented to demonstrate the effectiveness and advantages of GFE-Net. Compared with state-of-the-art algorithms, GFE-Net achieves superior performance in data dependency, enhancement performance, deployment efficiency, and scale generalizability. Follow-up fundus image analysis is also facilitated by GFE-Net, whose modules are respectively verified to be effective for image enhancement.Comment: Accepted by Medical Image Analysis in Auguest, 202

Retinal Fundus Image Quality Adjustment with Opponent Color Model

วิทยาศาสตรมหาบัณทิต (วิทยาการคอมพิวเตอร์),2565WHO reported the number of 65 million of Age-related Macular Degeneration (AMD) patients around the world, and expected the number would increase to 300 million patients by the year 2040. Currently, ophthalmologists rely on retinal fundus photographs to analyze AMD lesions. Nevertheless, sometimes the photographs have an unsatisfactory quality such as low contrast, under or over exposure which results in difficulties for the experts to analyze lesions. So, it is suggested to have the unsatisfactory photographs improved to enhance anatomical details appearance before use by the experts. This thesis proposed an effective retinal fundus image simulation modeling to enhance contrast and adjust the color balance. It is aimed to assist ophthalmologists in AMD lesion screening. The proposed method consists of a few steps to achieve the intent. Firstly, an input image is improved contrast with CLAHE technique by using CIE L^* a^* b^* color space. Then, the histogram of the output image from previous step is stretched and rescaled by a scaling histogram technique to adjust its overall brightness offset to meet the Hubbard’s retinal fundus image proper range standard. This thesis used images as experimental data from two datasets, DiaretDB0 and STARE datasets. The results indicate the proposed method yields a highly contrast and color-balance output which fits the Hubbard’s standard and easier to screen lesions.กองทุนวิจัยคณะวิทยาศาสตร์ มหาวิทยาลัยสงขลานครินทร์ สัญญาเลขที่ 2-2561-02-017องค์การอนามัยโลกหรือ WHO ได้รายงานจำนวนผู้ป่วยโรคจุดภาพชัดที่จอตาเสื่อมในผู้สูงอายุ (AMD) จำนวน 65 ล้านรายจากทั่วโลก และตัวเลขจะเพิ่มสูงขึ้นถึง 300 ล้านรายภายในปี ค.ศ. 2040 ในปัจจุบันการวิเคราะห์รอยโรค AMD นั้นใช้การวิเคราะห์ภาพถ่ายสีจอตา ซึ่งบางครั้งภาพถ่ายที่ได้นั้นมีคุณภาพที่ต่ำ เช่น มีคอนทราสต์ที่ต่ำ มีแสงที่มืดหรือสว่างเกินไป เป็นต้น ซึ่งจะทำให้ผู้เชี่ยวชาญวิเคราะห์รอยโรคจากภาพถ่ายนั้นได้ยาก ดังนั้นจึงจำเป็นที่จะต้องทำการปรับปรุงคุณภาพของภาพถ่ายเหล่านี้เพื่อทำให้รายละเอียดทางกายวิภาคดีขึ้นก่อนที่จะให้ผู้เชี่ยวชาญทำการวิเคราะห์รอยโรคต่อไป งานวิจัยชิ้นนี้จึงนำเสนอแบบจำลองเพื่อการปรับปรุงคอนทราสต์และสมดุลสีของภาพถ่ายสีจอตาที่มีประสิทธิภาพ เป้าหมายของงานวิจัยชิ้นนี้เพื่อช่วยผู้เชี่ยวชาญคัดกรองรอยโรค AMD โดยขั้นตอนวิธีของงานวิจัยประกอบด้วย ขั้นตอนแรกจะทำการปรับปรุงคอนทราสต์ของภาพถ่ายด้วยเทคนิค CLAHE โดยใช้แบบจำลองสี CIE L^* a^* b^* และขั้นตอนถัดไปจะทำการยืดและสเกลฮิสโทแกรมของภาพใหม่ด้วยเทคนิคการสเกลฮิสโทแกรมเพื่อปรับปรุงออฟเซตความสว่างโดยรวมของภาพถ่ายให้เป็นตามมาตรฐานช่วงความสว่างของภาพถ่ายสีจอตาที่ดีของ Hubbard งานวิจัยชิ้นนี้ใช้ภาพถ่ายสีจอตาในการทดลองจากสองชุดข้อมูล ได้แก่ ชุดข้อมูล DiaretDB0 และชุดข้อมูล STARE ผลการทดลองแสดงให้เห็นว่าวิธีที่นำเสนอให้ภาพผลลัพธ์ที่มีคอนทราสต์และสมดุลสีที่ดีขึ้นและเหมาะสมสำหรับใช้ในการวิเคราะห์รอยโรคตามมาตรฐานของ Hubbar

Segmentation of roots in soil with U-Net

Demonstration of the feasibility of a U-Net based CNN system for segmenting images of roots in soil and for replacing the manual line-intersect method

Patch-based Denoising Algorithms for Single and Multi-view Images

In general, all single and multi-view digital images are captured using sensors, where they are often contaminated with noise, which is an undesired random signal. Such noise can also be produced during transmission or by lossy image compression. Reducing the noise and enhancing those images is among the fundamental digital image processing tasks. Improving the performance of image denoising methods, would greatly contribute to single or multi-view image processing techniques, e.g. segmentation, computing disparity maps, etc. Patch-based denoising methods have recently emerged as the state-of-the-art denoising approaches for various additive noise levels. This thesis proposes two patch-based denoising methods for single and multi-view images, respectively. A modification to the block matching 3D algorithm is proposed for single image denoising. An adaptive collaborative thresholding filter is proposed which consists of a classification map and a set of various thresholding levels and operators. These are exploited when the collaborative hard-thresholding step is applied. Moreover, the collaborative Wiener filtering is improved by assigning greater weight when dealing with similar patches. For the denoising of multi-view images, this thesis proposes algorithms that takes a pair of noisy images captured from two different directions at the same time (stereoscopic images). The structural, maximum difference or the singular value decomposition-based similarity metrics is utilized for identifying locations of similar search windows in the input images. The non-local means algorithm is adapted for filtering these noisy multi-view images. The performance of both methods have been evaluated both quantitatively and qualitatively through a number of experiments using the peak signal-to-noise ratio and the mean structural similarity measure. Experimental results show that the proposed algorithm for single image denoising outperforms the original block matching 3D algorithm at various noise levels. Moreover, the proposed algorithm for multi-view image denoising can effectively reduce noise and assist to estimate more accurate disparity maps at various noise levels

Фізика з основами біофізики

The text-book "Physics with Fundamentals of Biophysics" published in English is intended for the students who attend the English-speaking lectures in educational institutions of Ukraine; it can be useful for the foreign students and post-graduate students, translators and everybody who is interested in English terminology in the field of physics and biophysics. The main objectives of the course “Physics with Fundamentals of Biophysics” is to expose principal laws and theses of physics which make it possible to study general regularities of natural phenomena; to apply the principles and methods of the physical sciences to biological problems; to consider the biophysical problems which are concerned with the viability of living objects (plants, animals, microorganisms) and their interaction with the environment; to elucidate possible application of physical instrumentation to agricultural, biological, ecological, and medical practice. The text-book is supplied with the examples of solutions of practical biophysical problems, control questions pertaining to those problems that require clarification. Rating system of estimation of students´ level of knowledge is offered also. Each text modulus contains the vocabulary of physical and biophysical terms. The informative material is given in appendix.Даний підручник виданий англійською мовою, призначений саме для підготовки студентів, що слухають лекції англійською мовою в навчальних закладах ІІІ-IV рівнів акредитації України. Він може бути корисним для іноземних студентів та аспірантів, перекладачів та всіх, хто цікавиться англомовною термінологією в галузі фізики та біофізики. Основна мета підручника - навести основні положення, закони та теорії з курсу загальної фізики; розглянути фізичні процеси та механізми, що складають основу життєдіяльності живих організмів – рослин, тварин, мікроорганізмів; викласти проблеми впливу зовнішніх фізичних факторів на живі організми та їх здатності реагувати на ці фактори; висвітлити принципи дії та можливі застосування сучасних фізичних методів та приладів у сільськогосподарській, біологічній, екологічній та медичній практиці. Підручник містить приклади розв’язання практичних біофізичних проблем, контрольні завдання для перевірки засвоєння матеріалу студентами та запитання, відповіді на які студенти зможуть дати у разі ознайомлення із відповідними розділами підручника. Для оцінки знань студентів пропонується рейтингова система. Кожний змістовний модуль має словник фізичних та біофізичних термінів. Інформативний матеріал представлений у додатку

Advanced Knowledge Application in Practice

The integration and interdependency of the world economy leads towards the creation of a global market that offers more opportunities, but is also more complex and competitive than ever before. Therefore widespread research activity is necessary if one is to remain successful on the market. This book is the result of research and development activities from a number of researchers worldwide, covering concrete fields of research

Extracting root system architecture from X-ray micro computed tomography images using visual tracking

X-ray micro computed tomography (µCT) is increasingly applied in plant biology as an imaging system that is valuable for the study of root development in soil, since it allows the three-dimensional and non-destructive visualisation of plant root systems. Variations in the X-ray attenuation values of root material and the overlap in measured intensity values between roots and soil caused by water and organic matter represent major challenges to the extraction of root system architecture. We propose a novel technique to recover root system information from X-ray CT data, using a strategy based on a visual tracking framework embedding a modiffed level set method that is evolved using the Jensen-Shannon divergence. The model-guided search arising from the visual tracking approach makes the method less sensitive to the natural ambiguity of X-ray attenuation values in the image data and thus allows a better extraction of the root system. The method is extended by mechanisms that account for plagiatropic response in roots as well as collision between root objects originating from different plants that are grown and interact within the same soil environment. Experimental results on monocot and dicot plants, grown in different soil textural types, show the ability of successfully extracting root system information. Various global root system traits are measured from the extracted data and compared to results obtained with alternative methods

Exploring cognition in visual search and vigilance tasks with eye tracking and pupillometry

Recent findings in experimental psychology suggest that pupillometry, the measurement of pupil size, can provide insight into cognitive processes associated with effort and target detection in visual search tasks and monitoring performance in vigilance tasks. With the increasing availability, affordability and flexibility of video-based eye tracking hardware, these experimental findings point to lucrative practical applications such as real-time biobehavioural monitoring systems to assist with socially important tasks in operational settings. The aim of the current thesis was to explore this potential with further experimental work paying close attention to methodological issues which complicate cognitive interpretations of pupillary responses, such as physical stimulus confounds and eye movement-related measurement error in video-based systems. Six original experiments were designed to specifically explore the relationship between pupil size, cognition and behavioural performance in classic visual search and vigilance paradigms. Experiments 1-2 examined the pupillometric effects of effort and target detection in visual search with briefly presented stimuli. Pupil responses showed small variability with respect to manipulations of set size and target presence but were influenced substantially by the requirement for a motor response. Experiments 3-4 explored the cognitive pupil dynamics of free-viewing visual search with data-driven correction for eye movement artefacts. Group-level averages revealed small transient pupil dilations following fixations on targets but not distractors, an effect which was not contingent on a motor response or correction for gaze position artefacts. Experiments 5-6 looked at the relationship between pupil size and detection performance measures in two types of vigilance task. Changes in baseline and stimulus-evoked pupil responses loosely mirrored changes in performance, but the relationships were neither linear nor consistent. Overall, the thesis affirms the practical potential for using cognitive pupillometry in research and applied settings, but emphasises the constraints arising from methodological and theoretical limitations

Preclinical validation of the possible mechanisms of Anti-Hypertensive, Diuretic and Anti-oxidant Activity of Venthamaraiyathi Chooranam in Rodents

The trial drug Venthamaraiyathi Chooranam was selected from the siddha literature “Pharmacopoeia of Hospital of Indian Medicine” authored by Dr.Narayanaswami for Anti-hypertensive, Diuretic, Anti-oxidant activities. The dissertation started with an introduction explaining about the siddha concept, prevalence of hypertension and role of the test drug in treating hypertension, ➢ The test drug was prepared properly by the given procedure. All the ingredients were identified and authenticated by the experts. ➢ Review of literature in various categories was carried out. Siddha aspect, botanical aspect and pharmaceutical review disclosed about the drug and the disease. Pharmacological review was done to establish the methodologies. ➢ The drug was subjected to analysis such as organoleptic characters, physicochemical, phytochemical, biochemical and also instrumental analysis which provided the key ingredients present in the drug thus it accounts the efficacy of the drug ➢ Toxicological study was made according to OECD guidelines comprising both acute and sub-acute toxicity study. It showed the safety of the drug which attributes its utility in long time administration. ➢ Pharmacological study was done. It revealed the Anti-hypertensive, Diuretic and Anti-oxidant activity (In–vitro model) of Venthamaraiyathi Chooranam in spontaneously hypertensive rat model. ➢ Results and discussion gives the necessary justifications to prove the potency of the drug. ➢ Conclusion gives a compiled form of the study and explains the synergistic effect of all the key ingredients and activities that supports the study. ➢ Thus, the Polyherbal formulation venthamaraiyathi chooranam is validated for its safety and efficacy for treating hypertension and it would be a one of the drugs of choice