Differently stained whole slide image registration technique with landmark validation

Abstract. One of the most significant features in digital pathology is to compare and fuse successive differently stained tissue sections, also called slides, visually. Doing so, aligning different images to a common frame, ground truth, is required. Current sample scanning tools enable to create images full of informative layers of digitalized tissues, stored with a high resolution into whole slide images. However, there are a limited amount of automatic alignment tools handling large images precisely in acceptable processing time. The idea of this study is to propose a deep learning solution for histopathology image registration. The main focus is on the understanding of landmark validation and the impact of stain augmentation on differently stained histopathology images. Also, the developed registration method is compared with the state-of-the-art algorithms which utilize whole slide images in the field of digital pathology. There are previous studies about histopathology, digital pathology, whole slide imaging and image registration, color staining, data augmentation, and deep learning that are referenced in this study. The goal is to develop a learning-based registration framework specifically for high-resolution histopathology image registration. Different whole slide tissue sample images are used with a resolution of up to 40x magnification. The images are organized into sets of consecutive, differently dyed sections, and the aim is to register the images based on only the visible tissue and ignore the background. Significant structures in the tissue are marked with landmarks. The quality measurements include, for example, the relative target registration error, structural similarity index metric, visual evaluation, landmark-based evaluation, matching points, and image details. These results are comparable and can be used also in the future research and in development of new tools. Moreover, the results are expected to show how the theory and practice are combined in whole slide image registration challenges. DeepHistReg algorithm will be studied to better understand the development of stain color feature augmentation-based image registration tool of this study. Matlab and Aperio ImageScope are the tools to annotate and validate the image, and Python is used to develop the algorithm of this new registration tool. As cancer is globally a serious disease regardless of age or lifestyle, it is important to find ways to develop the systems experts can use while working with patients’ data. There is still a lot to improve in the field of digital pathology and this study is one step toward it.Eri menetelmin värjättyjen virtuaalinäytelasien rekisteröintitekniikka kiintopisteiden validointia hyödyntäen. Tiivistelmä. Yksi tärkeimmistä digitaalipatologian ominaisuuksista on verrata ja fuusioida peräkkäisiä eri menetelmin värjättyjä kudosleikkeitä toisiinsa visuaalisesti. Tällöin keskenään lähes identtiset kuvat kohdistetaan samaan yhteiseen kehykseen, niin sanottuun pohjatotuuteen. Nykyiset näytteiden skannaustyökalut mahdollistavat sellaisten kuvien luonnin, jotka ovat täynnä kerroksittaista tietoa digitalisoiduista näytteistä, tallennettuna erittäin korkean resoluution virtuaalisiin näytelaseihin. Tällä hetkellä on olemassa kuitenkin vain kourallinen automaattisia työkaluja, jotka kykenevät käsittelemään näin valtavia kuvatiedostoja tarkasti hyväksytyin aikarajoin. Tämän työn tarkoituksena on syväoppimista hyväksikäyttäen löytää ratkaisu histopatologisten kuvien rekisteröintiin. Tärkeimpänä osa-alueena on ymmärtää kiintopisteiden validoinnin periaatteet sekä eri väriaineiden augmentoinnin vaikutus. Lisäksi tässä työssä kehitettyä rekisteröintialgoritmia tullaan vertailemaan muihin kirjallisuudessa esitettyihin algoritmeihin, jotka myös hyödyntävät virtuaalinäytelaseja digitaalipatologian saralla. Kirjallisessa osiossa tullaan siteeraamaan aiempia tutkimuksia muun muassa seuraavista aihealueista: histopatologia, digitaalipatologia, virtuaalinäytelasi, kuvantaminen ja rekisteröinti, näytteen värjäys, data-augmentointi sekä syväoppiminen. Tavoitteena on kehittää oppimispohjainen rekisteröintikehys erityisesti korkearesoluutioisille digitalisoiduille histopatologisille kuville. Erilaisissa näytekuvissa tullaan käyttämään jopa 40-kertaista suurennosta. Kuvat kudoksista on järjestetty eri menetelmin värjättyihin peräkkäisiin kuvasarjoihin ja tämän työn päämääränä on rekisteröidä kuvat pohjautuen ainoastaan kudosten näkyviin osuuksiin, jättäen kuvien tausta huomioimatta. Kudosten merkittävimmät rakenteet on merkattu niin sanotuin kiintopistein. Työn laatumittauksina käytetään arvoja, kuten kohteen suhteellinen rekisteröintivirhe (rTRE), rakenteellisen samankaltaisuuindeksin mittari (SSIM), sekä visuaalista arviointia, kiintopisteisiin pohjautuvaa arviointia, yhteensopivuuskohtia, ja kuvatiedoston yksityiskohtia. Nämä arvot ovat verrattavissa myös tulevissa tutkimuksissa ja samaisia arvoja voidaan käyttää uusia työkaluja kehiteltäessä. DeepHistReg metodi toimii pohjana tässä työssä kehitettävälle näytteen värjäyksen parantamiseen pohjautuvalle rekisteröintityökalulle. Matlab ja Aperio ImageScope ovat ohjelmistoja, joita tullaan hyödyntämään tässä työssä kuvien merkitsemiseen ja validointiin. Ohjelmointikielenä käytetään Pythonia. Syöpä on maailmanlaajuisesti vakava sairaus, joka ei katso ikää eikä elämäntyyliä. Siksi on tärkeää löytää uusia keinoja kehittää työkaluja, joita asiantuntijat voivat hyödyntää jokapäiväisessä työssään potilastietojen käsittelyssä. Digitaalipatologian osa-alueella on vielä paljon innovoitavaa ja tämä työ on yksi askel eteenpäin taistelussa syöpäsairauksia vastaan

Quantifying scribal behavior : a novel approach to digital paleography

We propose a novel approach for analyzing scribal behavior quantitatively using information about the handwriting of characters. To implement this approach, we develop a computational framework that recovers this information and decomposes the characters into primitives (called strokes) to create a hierarchically structured representation. We then propose a number of intuitive metrics quantifying various facets of scribal behavior, which are derived from the recovered information and character structure. We further propose the use of techniques modeling the generation of handwriting to directly study the changes in writing behavior. We then present a case study in which we use our framework and metrics to analyze the development of four major Indic scripts. We show that our framework and metrics coupled with appropriate statistical methods can provide great insight into scribal behavior by discovering specific trends and phenomena with quantitative methods. We also illustrate the use of handwriting modeling techniques in this context to study the divergence of the Brahmi script into two daughter scripts. We conduct a user study with domain experts to evaluate our framework and salient results from the case study, and we elaborate on the results of this evaluation. Finally, we present our conclusions and discuss the limitations of our research along with future work that needs to be done

AutoGraff: towards a computational understanding of graffiti writing and related art forms.

The aim of this thesis is to develop a system that generates letters and pictures with a style that is immediately recognizable as graffiti art or calligraphy. The proposed system can be used similarly to, and in tight integration with, conventional computer-aided geometric design tools and can be used to generate synthetic graffiti content for urban environments in games and in movies, and to guide robotic or fabrication systems that can materialise the output of the system with physical drawing media. The thesis is divided into two main parts. The first part describes a set of stroke primitives, building blocks that can be combined to generate different designs that resemble graffiti or calligraphy. These primitives mimic the process typically used to design graffiti letters and exploit well known principles of motor control to model the way in which an artist moves when incrementally tracing stylised letter forms. The second part demonstrates how these stroke primitives can be automatically recovered from input geometry defined in vector form, such as the digitised traces of writing made by a user, or the glyph outlines in a font. This procedure converts the input geometry into a seed that can be transformed into a variety of calligraphic and graffiti stylisations, which depend on parametric variations of the strokes

Forging a Stable Relationship?: Bridging the Law and Forensic Science Divide in the Academy

The marriage of law and science has most often been represented as discordant. While the law/science divide meme is hardly novel, concerns over the potentially deleterious coupling within the criminal justice system may have reached fever pitch. There is a growing chorus of disapproval addressed to ‘forensic science’, accompanied by the denigration of legal professionals for being unable or unwilling to forge a symbiotic relationship with forensic scientists. The 2009 National Academy of Sciences Report on forensic science heralds the latest call for greater collaboration between ‘law’ and ‘science’, particularly in Higher Education Institutions (HEIs) yet little reaction has been apparent amid law and science faculties. To investigate the potential for interdisciplinary cooperation, the authors received funding for a project: ‘Lowering the Drawbridges: Forensic and Legal Education in the 21st Century’, hoping to stimulate both law and forensic science educators to seek mutually beneficial solutions to common educational problems and build vital connections in the academy. A workshop held in the UK, attended by academics and practitioners from scientific, policing, and legal backgrounds marked the commencement of the project. This paper outlines some of the workshop conclusions to elucidate areas of dissent and consensus, and where further dialogue is required, but aims to strike a note of optimism that the ‘cultural divide’ should not be taken to be so wide as to be beyond the legal and forensic science academy to bridge. The authors seek to demonstrate that legal and forensic science educators can work cooperatively to respond to critics and forge new paths in learning and teaching, creating an opportunity to take stock and enrich our discipline as well as answer critics. As Latham (2010:34) exhorts, we are not interested in turning lawyers into scientists and vice versa, but building a foundation upon which they can build during their professional lives: “Instead of melding the two cultures, we need to establish conditions of cooperation, mutual respect, and mutual reliance between them.” Law and forensic science educators should, and can assist with the building of a mutual understanding between forensic scientists and legal professionals, a significant step on the road to answering calls for the professions to minimise some of the risks associated with the use of forensic science in the criminal process. REFERENCES Latham, S.R. 2010, ‘Law between the cultures: C.P.Snow’s The Two Cultures and the problem of scientific illiteracy in law’ 32 Technology in Society, 31-34. KEYWORDS forensic science education legal education law/science divid

Exploiting Spatio-Temporal Coherence for Video Object Detection in Robotics

This paper proposes a method to enhance video object detection for indoor environments in robotics. Concretely, it exploits knowledge about the camera motion between frames to propagate previously detected objects to successive frames. The proposal is rooted in the concepts of planar homography to propose regions of interest where to find objects, and recursive Bayesian filtering to integrate observations over time. The proposal is evaluated on six virtual, indoor environments, accounting for the detection of nine object classes over a total of ∼ 7k frames. Results show that our proposal improves the recall and the F1-score by a factor of 1.41 and 1.27, respectively, as well as it achieves a significant reduction of the object categorization entropy (58.8%) when compared to a two-stage video object detection method used as baseline, at the cost of small time overheads (120 ms) and precision loss (0.92).</p

Towards robust real-world historical handwriting recognition

In this thesis, we make a bridge from the past to the future by using artificial-intelligence methods for text recognition in a historical Dutch collection of the Natuurkundige Commissie that explored Indonesia (1820-1850). In spite of the successes of systems like 'ChatGPT', reading historical handwriting is still quite challenging for AI. Whereas GPT-like methods work on digital texts, historical manuscripts are only available as an extremely diverse collections of (pixel) images. Despite the great results, current DL methods are very data greedy, time consuming, heavily dependent on the human expert from the humanities for labeling and require machine-learning experts for designing the models. Ideally, the use of deep learning methods should require minimal human effort, have an algorithm observe the evolution of the training process, and avoid inefficient use of the already sparse amount of labeled data. We present several approaches towards dealing with these problems, aiming to improve the robustness of current methods and to improve the autonomy in training. We applied our novel word and line text recognition approaches on nine data sets differing in time period, language, and difficulty: three locally collected historical Latin-based data sets from Naturalis, Leiden; four public Latin-based benchmark data sets for comparability with other approaches; and two Arabic data sets. Using ensemble voting of just five neural networks, a level of accuracy was achieved which required hundreds of neural networks in earlier studies. Moreover, we increased the speed of evaluation of each training epoch without the need of labeled data

Biometrics

Biometrics uses methods for unique recognition of humans based upon one or more intrinsic physical or behavioral traits. In computer science, particularly, biometrics is used as a form of identity access management and access control. It is also used to identify individuals in groups that are under surveillance. The book consists of 13 chapters, each focusing on a certain aspect of the problem. The book chapters are divided into three sections: physical biometrics, behavioral biometrics and medical biometrics. The key objective of the book is to provide comprehensive reference and text on human authentication and people identity verification from both physiological, behavioural and other points of view. It aims to publish new insights into current innovations in computer systems and technology for biometrics development and its applications. The book was reviewed by the editor Dr. Jucheng Yang, and many of the guest editors, such as Dr. Girija Chetty, Dr. Norman Poh, Dr. Loris Nanni, Dr. Jianjiang Feng, Dr. Dongsun Park, Dr. Sook Yoon and so on, who also made a significant contribution to the book