The malaria system microApp: A new, mobile device-based tool for malaria diagnosis

Background: Malaria is a public health problem that affects remote areas worldwide. Climate change has contributed to the problem by allowing for the survival of Anopheles in previously uninhabited areas. As such, several groups have made developing news systems for the automated diagnosis of malaria a priority. Objective: The objective of this study was to develop a new, automated, mobile device-based diagnostic system for malaria. The system uses Giemsa-stained peripheral blood samples combined with light microscopy to identify the Plasmodium falciparum species in the ring stage of development. Methods: The system uses image processing and artificial intelligence techniques as well as a known face detection algorithm to identify Plasmodium parasites. The algorithm is based on integral image and haar-like features concepts, and makes use of weak classifiers with adaptive boosting learning. The search scope of the learning algorithm is reduced in the preprocessing step by removing the background around blood cells. Results: As a proof of concept experiment, the tool was used on 555 malaria-positive and 777 malaria-negative previously-made slides. The accuracy of the system was, on average, 91%, meaning that for every 100 parasite-infected samples, 91 were identified correctly. Conclusions: Accessibility barriers of low-resource countries can be addressed with low-cost diagnostic tools. Our system, developed for mobile devices (mobile phones and tablets), addresses this by enabling access to health centers in remote communities, and importantly, not depending on extensive malaria expertise or expensive diagnostic detection equipment.Peer ReviewedPostprint (published version

Deep Neural Networks for Document Processing of Music Score Images

[EN] There is an increasing interest in the automatic digitization of medieval music documents. Despite efforts in this field, the detection of the different layers of information on these documents still poses difficulties. The use of Deep Neural Networks techniques has reported outstanding results in many areas related to computer vision. Consequently, in this paper, we study the so-called Convolutional Neural Networks (CNN) for performing the automatic document processing of music score images. This process is focused on layering the image into its constituent parts (namely, background, staff lines, music notes, and text) by training a classifier with examples of these parts. A comprehensive experimentation in terms of the configuration of the networks was carried out, which illustrates interesting results as regards to both the efficiency and effectiveness of these models. In addition, a cross-manuscript adaptation experiment was presented in which the networks are evaluated on a different manuscript from the one they were trained. The results suggest that the CNN is capable of adapting its knowledge, and so starting from a pre-trained CNN reduces (or eliminates) the need for new labeled data.This work was supported by the Social Sciences and Humanities Research Council of Canada, and Universidad de Alicante through grant GRE-16-04.Calvo-Zaragoza, J.; Castellanos, F.; Vigliensoni, G.; Fujinaga, I. (2018). Deep Neural Networks for Document Processing of Music Score Images. Applied Sciences. 8(5). https://doi.org/10.3390/app8050654S85Bainbridge, D., & Bell, T. (2001). Computers and the Humanities, 35(2), 95-121. doi:10.1023/a:1002485918032Byrd, D., & Simonsen, J. G. (2015). Towards a Standard Testbed for Optical Music Recognition: Definitions, Metrics, and Page Images. Journal of New Music Research, 44(3), 169-195. doi:10.1080/09298215.2015.1045424LeCun, Y., Bengio, Y., & Hinton, G. (2015). Deep learning. Nature, 521(7553), 436-444. doi:10.1038/nature14539Rebelo, A., Fujinaga, I., Paszkiewicz, F., Marcal, A. R. S., Guedes, C., & Cardoso, J. S. (2012). Optical music recognition: state-of-the-art and open issues. International Journal of Multimedia Information Retrieval, 1(3), 173-190. doi:10.1007/s13735-012-0004-6Louloudis, G., Gatos, B., Pratikakis, I., & Halatsis, C. (2008). Text line detection in handwritten documents. Pattern Recognition, 41(12), 3758-3772. doi:10.1016/j.patcog.2008.05.011Montagner, I. S., Hirata, N. S. T., & Hirata, R. (2017). Staff removal using image operator learning. Pattern Recognition, 63, 310-320. doi:10.1016/j.patcog.2016.10.002Calvo-Zaragoza, J., Micó, L., & Oncina, J. (2016). Music staff removal with supervised pixel classification. International Journal on Document Analysis and Recognition (IJDAR), 19(3), 211-219. doi:10.1007/s10032-016-0266-2Calvo-Zaragoza, J., Pertusa, A., & Oncina, J. (2017). Staff-line detection and removal using a convolutional neural network. Machine Vision and Applications, 28(5-6), 665-674. doi:10.1007/s00138-017-0844-4Shelhamer, E., Long, J., & Darrell, T. (2017). Fully Convolutional Networks for Semantic Segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 39(4), 640-651. doi:10.1109/tpami.2016.2572683Kato, Z. (2011). Markov Random Fields in Image Segmentation. Foundations and Trends® in Signal Processing, 5(1-2), 1-155. doi:10.1561/2000000035Lecun, Y., Bottou, L., Bengio, Y., & Haffner, P. (1998). Gradient-based learning applied to document recognition. Proceedings of the IEEE, 86(11), 2278-2324. doi:10.1109/5.72679

Adaptive Methods for Robust Document Image Understanding

A vast amount of digital document material is continuously being produced as part of major digitization efforts around the world. In this context, generic and efficient automatic solutions for document image understanding represent a stringent necessity. We propose a generic framework for document image understanding systems, usable for practically any document types available in digital form. Following the introduced workflow, we shift our attention to each of the following processing stages in turn: quality assurance, image enhancement, color reduction and binarization, skew and orientation detection, page segmentation and logical layout analysis. We review the state of the art in each area, identify current defficiencies, point out promising directions and give specific guidelines for future investigation. We address some of the identified issues by means of novel algorithmic solutions putting special focus on generality, computational efficiency and the exploitation of all available sources of information. More specifically, we introduce the following original methods: a fully automatic detection of color reference targets in digitized material, accurate foreground extraction from color historical documents, font enhancement for hot metal typesetted prints, a theoretically optimal solution for the document binarization problem from both computational complexity- and threshold selection point of view, a layout-independent skew and orientation detection, a robust and versatile page segmentation method, a semi-automatic front page detection algorithm and a complete framework for article segmentation in periodical publications. The proposed methods are experimentally evaluated on large datasets consisting of real-life heterogeneous document scans. The obtained results show that a document understanding system combining these modules is able to robustly process a wide variety of documents with good overall accuracy

Neural Networks for Document Image and Text Processing

Nowadays, the main libraries and document archives are investing a considerable effort on digitizing their collections. Indeed, most of them are scanning the documents and publishing the resulting images without their corresponding transcriptions. This seriously limits the document exploitation possibilities. When the transcription is necessary, it is manually performed by human experts, which is a very expensive and error-prone task. Obtaining transcriptions to the level of required quality demands the intervention of human experts to review and correct the resulting output of the recognition engines. To this end, it is extremely useful to provide interactive tools to obtain and edit the transcription. Although text recognition is the final goal, several previous steps (known as preprocessing) are necessary in order to get a fine transcription from a digitized image. Document cleaning, enhancement, and binarization (if they are needed) are the first stages of the recognition pipeline. Historical Handwritten Documents, in addition, show several degradations, stains, ink-trough and other artifacts. Therefore, more sophisticated and elaborate methods are required when dealing with these kind of documents, even expert supervision in some cases is needed. Once images have been cleaned, main zones of the image have to be detected: those that contain text and other parts such as images, decorations, versal letters. Moreover, the relations among them and the final text have to be detected. Those preprocessing steps are critical for the final performance of the system since an error at this point will be propagated during the rest of the transcription process. The ultimate goal of the Document Image Analysis pipeline is to receive the transcription of the text (Optical Character Recognition and Handwritten Text Recognition). During this thesis we aimed to improve the main stages of the recognition pipeline, from the scanned documents as input to the final transcription. We focused our effort on applying Neural Networks and deep learning techniques directly on the document images to extract suitable features that will be used by the different tasks dealt during the following work: Image Cleaning and Enhancement (Document Image Binarization), Layout Extraction, Text Line Extraction, Text Line Normalization and finally decoding (or text line recognition). As one can see, the following work focuses on small improvements through the several Document Image Analysis stages, but also deals with some of the real challenges: historical manuscripts and documents without clear layouts or very degraded documents. Neural Networks are a central topic for the whole work collected in this document. Different convolutional models have been applied for document image cleaning and enhancement. Connectionist models have been used, as well, for text line extraction: first, for detecting interest points and combining them in text segments and, finally, extracting the lines by means of aggregation techniques; and second, for pixel labeling to extract the main body area of the text and then the limits of the lines. For text line preprocessing, i.e., to normalize the text lines before recognizing them, similar models have been used to detect the main body area and then to height-normalize the images giving more importance to the central area of the text. Finally, Convolutional Neural Networks and deep multilayer perceptrons have been combined with hidden Markov models to improve our transcription engine significantly. The suitability of all these approaches has been tested with different corpora for any of the stages dealt, giving competitive results for most of the methodologies presented.Hoy en día, las principales librerías y archivos está invirtiendo un esfuerzo considerable en la digitalización de sus colecciones. De hecho, la mayoría están escaneando estos documentos y publicando únicamente las imágenes sin transcripciones, limitando seriamente la posibilidad de explotar estos documentos. Cuando la transcripción es necesaria, esta se realiza normalmente por expertos de forma manual, lo cual es una tarea costosa y propensa a errores. Si se utilizan sistemas de reconocimiento automático se necesita la intervención de expertos humanos para revisar y corregir la salida de estos motores de reconocimiento. Por ello, es extremadamente útil para proporcionar herramientas interactivas con el fin de generar y corregir la transcripciones. Aunque el reconocimiento de texto es el objetivo final del Análisis de Documentos, varios pasos previos (preprocesamiento) son necesarios para conseguir una buena transcripción a partir de una imagen digitalizada. La limpieza, mejora y binarización de las imágenes son las primeras etapas del proceso de reconocimiento. Además, los manuscritos históricos tienen una mayor dificultad en el preprocesamiento, puesto que pueden mostrar varios tipos de degradaciones, manchas, tinta a través del papel y demás dificultades. Por lo tanto, este tipo de documentos requiere métodos de preprocesamiento más sofisticados. En algunos casos, incluso, se precisa de la supervisión de expertos para garantizar buenos resultados en esta etapa. Una vez que las imágenes han sido limpiadas, las diferentes zonas de la imagen deben de ser localizadas: texto, gráficos, dibujos, decoraciones, letras versales, etc. Por otra parte, también es importante conocer las relaciones entre estas entidades. Estas etapas del pre-procesamiento son críticas para el rendimiento final del sistema, ya que los errores cometidos en aquí se propagarán al resto del proceso de transcripción. El objetivo principal del trabajo presentado en este documento es mejorar las principales etapas del proceso de reconocimiento completo: desde las imágenes escaneadas hasta la transcripción final. Nuestros esfuerzos se centran en aplicar técnicas de Redes Neuronales (ANNs) y aprendizaje profundo directamente sobre las imágenes de los documentos, con la intención de extraer características adecuadas para las diferentes tareas: Limpieza y Mejora de Documentos, Extracción de Líneas, Normalización de Líneas de Texto y, finalmente, transcripción del texto. Como se puede apreciar, el trabajo se centra en pequeñas mejoras en diferentes etapas del Análisis y Procesamiento de Documentos, pero también trata de abordar tareas más complejas: manuscritos históricos, o documentos que presentan degradaciones. Las ANNs y el aprendizaje profundo son uno de los temas centrales de esta tesis. Diferentes modelos neuronales convolucionales se han desarrollado para la limpieza y mejora de imágenes de documentos. También se han utilizado modelos conexionistas para la extracción de líneas: primero, para detectar puntos de interés y segmentos de texto y, agregarlos para extraer las líneas del documento; y en segundo lugar, etiquetando directamente los píxeles de la imagen para extraer la zona central del texto y así definir los límites de las líneas. Para el preproceso de las líneas de texto, es decir, la normalización del texto antes del reconocimiento final, se han utilizado modelos similares a los mencionados para detectar la zona central del texto. Las imagenes se rescalan a una altura fija dando más importancia a esta zona central. Por último, en cuanto a reconocimiento de escritura manuscrita, se han combinado técnicas de ANNs y aprendizaje profundo con Modelos Ocultos de Markov, mejorando significativamente los resultados obtenidos previamente por nuestro motor de reconocimiento. La idoneidad de todos estos enfoques han sido testeados con diferentes corpus en cada una de las tareas tratadas., obtenieAvui en dia, les principals llibreries i arxius històrics estan invertint un esforç considerable en la digitalització de les seues col·leccions de documents. De fet, la majoria estan escanejant aquests documents i publicant únicament les imatges sense les seues transcripcions, fet que limita seriosament la possibilitat d'explotació d'aquests documents. Quan la transcripció del text és necessària, normalment aquesta és realitzada per experts de forma manual, la qual cosa és una tasca costosa i pot provocar errors. Si s'utilitzen sistemes de reconeixement automàtic es necessita la intervenció d'experts humans per a revisar i corregir l'eixida d'aquests motors de reconeixement. Per aquest motiu, és extremadament útil proporcionar eines interactives amb la finalitat de generar i corregir les transcripcions generades pels motors de reconeixement. Tot i que el reconeixement del text és l'objectiu final de l'Anàlisi de Documents, diversos passos previs (coneguts com preprocessament) són necessaris per a l'obtenció de transcripcions acurades a partir d'imatges digitalitzades. La neteja, millora i binarització de les imatges (si calen) són les primeres etapes prèvies al reconeixement. A més a més, els manuscrits històrics presenten una major dificultat d'analisi i preprocessament, perquè poden mostrar diversos tipus de degradacions, taques, tinta a través del paper i altres peculiaritats. Per tant, aquest tipus de documents requereixen mètodes de preprocessament més sofisticats. En alguns casos, fins i tot, es precisa de la supervisió d'experts per a garantir bons resultats en aquesta etapa. Una vegada que les imatges han sigut netejades, les diferents zones de la imatge han de ser localitzades: text, gràfics, dibuixos, decoracions, versals, etc. D'altra banda, també és important conéixer les relacions entre aquestes entitats i el text que contenen. Aquestes etapes del preprocessament són crítiques per al rendiment final del sistema, ja que els errors comesos en aquest moment es propagaran a la resta del procés de transcripció. L'objectiu principal del treball que estem presentant és millorar les principals etapes del procés de reconeixement, és a dir, des de les imatges escanejades fins a l'obtenció final de la transcripció del text. Els nostres esforços se centren en aplicar tècniques de Xarxes Neuronals (ANNs) i aprenentatge profund directament sobre les imatges de documents, amb la intenció d'extraure característiques adequades per a les diferents tasques analitzades: neteja i millora de documents, extracció de línies, normalització de línies de text i, finalment, transcripció. Com es pot apreciar, el treball realitzat aplica xicotetes millores en diferents etapes de l'Anàlisi de Documents, però també tracta d'abordar tasques més complexes: manuscrits històrics, o documents que presenten degradacions. Les ANNs i l'aprenentatge profund són un dels temes centrals d'aquesta tesi. Diferents models neuronals convolucionals s'han desenvolupat per a la neteja i millora de les dels documents. També s'han utilitzat models connexionistes per a la tasca d'extracció de línies: primer, per a detectar punts d'interés i segments de text i, agregar-los per a extraure les línies del document; i en segon lloc, etiquetant directament els pixels de la imatge per a extraure la zona central del text i així definir els límits de les línies. Per al preprocés de les línies de text, és a dir, la normalització del text abans del reconeixement final, s'han utilitzat models similars als utilitzats per a l'extracció de línies. Finalment, quant al reconeixement d'escriptura manuscrita, s'han combinat tècniques de ANNs i aprenentatge profund amb Models Ocults de Markov, que han millorat significativament els resultats obtinguts prèviament pel nostre motor de reconeixement. La idoneïtat de tots aquests enfocaments han sigut testejats amb diferents corpus en cadascuna de les tasques tractadPastor Pellicer, J. (2017). Neural Networks for Document Image and Text Processing [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90443TESI

Analysis and Modular Approach for Text Extraction from Scientific Figures on Limited Data

Scientific figures are widely used as compact, comprehensible representations of important information. The re-usability of these figures is however limited, as one can rarely search directly for them, since they are mostly indexing by their surrounding text (e. g., publication or website) which often does not contain the full-message of the figure. In this thesis, the focus is on making the content of scientific figures accessible by extracting the text from these figures. A modular pipeline for unsupervised text extraction from scientific figures, based on a thorough analysis of the literature, was built to address the problem. This modular pipeline was used to build several unsupervised approaches, to evaluate different methods from the literature and new methods and method combinations. Some supervised approaches were built as well for comparison. One challenge, while evaluating the approaches, was the lack of annotated data, which especially needed to be considered when building the supervised approach. Three existing datasets were used for evaluation as well as two datasets of 241 scientific figures which were manually created and annotated. Additionally, two existing datasets for text extraction from other types of images were used for pretraining the supervised approach. Several experiments showed the superiority of the unsupervised pipeline over common Optical Character Recognition engines and identified the best unsupervised approach. This unsupervised approach was compared with the best supervised approach, which, despite of the limited amount of training data available, clearly outperformed the unsupervised approach.Infografiken sind ein viel verwendetes Medium zur kompakten Darstellung von Kernaussagen. Die Nachnutzbarkeit dieser Abbildungen ist jedoch häufig limitiert, da sie schlecht auffindbar sind, da sie meist über die umschließenden Medien, wie beispielsweise Publikationen oder Webseiten, und nicht über ihren Inhalt indexiert sind. Der Fokus dieser Arbeit liegt auf der Extraktion der textuellen Inhalte aus Infografiken, um deren Inhalt zu erschließen. Ausgehend von einer umfangreichen Analyse verwandter Arbeiten, wurde ein generalisierender, modularer Ansatz für die unüberwachte Textextraktion aus wissenschaftlichen Abbildungen entwickelt. Mit diesem modularen Ansatz wurden mehrere unüberwachte Ansätze und daneben auch noch einige überwachte Ansätze umgesetzt, um diverse Methoden aus der Literatur sowie neue und bisher noch nicht genutzte Methoden zu vergleichen. Eine Herausforderung bei der Evaluation war die geringe Menge an annotierten Abbildungen, was insbesondere beim überwachten Ansatz Methoden berücksichtigt werden musste. Für die Evaluation wurden drei existierende Datensätze verwendet und zudem wurden zusätzlich zwei Datensätze mit insgesamt 241 Infografiken erstellt und mit den nötigen Informationen annotiert, sodass insgesamt 5 Datensätze für die Evaluation verwendet werden konnten. Für das Pre-Training des überwachten Ansatzes wurden zudem zwei Datensätze aus verwandten Textextraktionsbereichen verwendet. In verschiedenen Experimenten wird gezeigt, dass der unüberwachte Ansatz besser funktioniert als klassische Texterkennungsverfahren und es wird aus den verschiedenen unüberwachten Ansätzen der beste ermittelt. Dieser unüberwachte Ansatz wird mit dem überwachten Ansatz verglichen, der trotz begrenzter Trainingsdaten die besten Ergebnisse liefert

Recognition of Characters from Streaming Videos

Non

Text Detection in Natural Scenes and Technical Diagrams with Convolutional Feature Learning and Cascaded Classification

An enormous amount of digital images are being generated and stored every day. Understanding text in these images is an important challenge with large impacts for academic, industrial and domestic applications. Recent studies address the difficulty of separating text targets from noise and background, all of which vary greatly in natural scenes. To tackle this problem, we develop a text detection system to analyze and utilize visual information in a data driven, automatic and intelligent way. The proposed method incorporates features learned from data, including patch-based coarse-to-fine detection (Text-Conv), connected component extraction using region growing, and graph-based word segmentation (Word-Graph). Text-Conv is a sliding window-based detector, with convolution masks learned using the Convolutional k-means algorithm (Coates et. al, 2011). Unlike convolutional neural networks (CNNs), a single vector/layer of convolution mask responses are used to classify patches. An initial coarse detection considers both local and neighboring patch responses, followed by refinement using varying aspect ratios and rotations for a smaller local detection window. Different levels of visual detail from ground truth are utilized in each step, first using constraints on bounding box intersections, and then a combination of bounding box and pixel intersections. Combining masks from different Convolutional k-means initializations, e.g., seeded using random vectors and then support vectors improves performance. The Word-Graph algorithm uses contextual information to improve word segmentation and prune false character detections based on visual features and spatial context. Our system obtains pixel, character, and word detection f-measures of 93.14%, 90.26%, and 86.77% respectively for the ICDAR 2015 Robust Reading Focused Scene Text dataset, out-performing state-of-the-art systems, and producing highly accurate text detection masks at the pixel level. To investigate the utility of our feature learning approach for other image types, we perform tests on 8- bit greyscale USPTO patent drawing diagram images. An ensemble of Ada-Boost classifiers with different convolutional features (MetaBoost) is used to classify patches as text or background. The Tesseract OCR system is used to recognize characters in detected labels and enhance performance. With appropriate pre-processing and post-processing, f-measures of 82% for part label location, and 73% for valid part label locations and strings are obtained, which are the best obtained to-date for the USPTO patent diagram data set used in our experiments. To sum up, an intelligent refinement of convolutional k-means-based feature learning and novel automatic classification methods are proposed for text detection, which obtain state-of-the-art results without the need for strong prior knowledge. Different ground truth representations along with features including edges, color, shape and spatial relationships are used coherently to improve accuracy. Different variations of feature learning are explored, e.g. support vector-seeded clustering and MetaBoost, with results suggesting that increased diversity in learned features benefit convolution-based text detectors

DocStormer: Revitalizing Multi-Degraded Colored Document Images to Pristine PDF

For capturing colored document images, e.g. posters and magazines, it is common that multiple degradations such as shadows, wrinkles, etc., are simultaneously introduced due to external factors. Restoring multi-degraded colored document images is a great challenge, yet overlooked, as most existing algorithms focus on enhancing color-ignored document images via binarization. Thus, we propose DocStormer, a novel algorithm designed to restore multi-degraded colored documents to their potential pristine PDF. The contributions are: firstly, we propose a "Perceive-then-Restore" paradigm with a reinforced transformer block, which more effectively encodes and utilizes the distribution of degradations. Secondly, we are the first to utilize GAN and pristine PDF magazine images to narrow the distribution gap between the enhanced results and PDF images, in pursuit of less degradation and better visual quality. Thirdly, we propose a non-parametric strategy, PFILI, which enables a smaller training scale and larger testing resolutions with acceptable detail trade-off, while saving memory and inference time. Fourthly, we are the first to propose a novel Multi-Degraded Colored Document image Enhancing dataset, named MD-CDE, for both training and evaluation. Experimental results show that the DocStormer exhibits superior performance, capable of revitalizing multi-degraded colored documents into their potential pristine digital versions, which fills the current academic gap from the perspective of method, data, and task