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Mireia Sole, Joan Blanco, Debora Gil, Oliver Valero, B. Cardenas, G. Fonseka, et al. (2022). Time to match; when do homologous chromosomes become closer? CHRO - Chromosoma, .
Abstract: In most eukaryotes, pairing of homologous chromosomes is an essential feature of meiosis that ensures homologous recombination and segregation. However, when the pairing process begins, it is still under investigation. Contrasting data exists in Mus musculus, since both leptotene DSB-dependent and preleptotene DSB-independent mechanisms have been described. To unravel this contention, we examined homologous pairing in pre-meiotic and meiotic Mus musculus cells using a threedimensional fuorescence in situ hybridization-based protocol, which enables the analysis of the entire karyotype using DNA painting probes. Our data establishes in an unambiguously manner that 73.83% of homologous chromosomes are already paired at premeiotic stages (spermatogonia-early preleptotene spermatocytes). The percentage of paired homologous chromosomes increases to 84.60% at mid-preleptotene-zygotene stage, reaching 100% at pachytene stage. Importantly, our results demonstrate a high percentage of homologous pairing observed before the onset of meiosis; this pairing does not occur randomly, as the percentage was higher than that observed in somatic cells (19.47%) and between nonhomologous chromosomes (41.1%). Finally, we have also observed that premeiotic homologous pairing is asynchronous and independent of the chromosome size, GC content, or presence of NOR regions.
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Mirko Arnold, Anarta Ghosh, Gerard Lacey, Stephen Patchett, & Hugh Mulcahy. (2009). Indistinct frame detection in colonoscopy videos. In Machine Vision and Image Processing Conference (pp. 47–52).
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Mirko Arnold, Anarta Ghosh, Glen Doherty, Hugh Mulcahy, Stephen Patchett, & Gerard Lacey. (2013). Towards Automatic Direct Observation of Procedure and Skill (DOPS) in Colonoscopy. In Proceedings of the International Conference on Computer Vision Theory and Applications (pp. 48–53).
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Mirko Arnold, Anarta Ghosh, Stephen Ameling, & G Lacey. (2010). Automatic segmentation and inpainting of specular highlights for endoscopic imaging. EURASIP JIVP - EURASIP Journal on Image and Video Processing, 2010(9).
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Mirko Arnold, Stephan Ameling, Anarta Ghosh, & Gerard Lacey. (2011). Quality Improvement of Endoscopy Videos. In Proceedings of the 8th IASTED International Conference on Biomedical Engineering (Vol. 723).
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Misael Rosales. (2002). Empirical Simulation Moldel of Intravascular Ultrasound.
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Misael Rosales. (2005). A Physics-Based Image Modelling of IVUS as a Geometric and Kinematic System (Petia Radeva, Ed.). Ph.D. thesis, , .
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Misael Rosales, & Petia Radeva. (2003). Empirical simulation model of intravascular ultrasound.
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Misael Rosales, Petia Radeva, J. Mauri, & Oriol Pujol. (2004). Simulation Model of Intravascular Ultrasound Images.
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Misael Rosales, Petia Radeva, Oriol Rodriguez-Leor, & Debora Gil. (2009). Modelling of image-catheter motion for 3-D IVUS. MIA - Medical image analysis, 13(1), 91–104.
Abstract: Three-dimensional intravascular ultrasound (IVUS) allows to visualize and obtain volumetric measurements of coronary lesions through an exploration of the cross sections and longitudinal views of arteries. However, the visualization and subsequent morpho-geometric measurements in IVUS longitudinal cuts are subject to distortion caused by periodic image/vessel motion around the IVUS catheter. Usually, to overcome the image motion artifact ECG-gating and image-gated approaches are proposed, leading to slowing the pullback acquisition or disregarding part of IVUS data. In this paper, we argue that the image motion is due to 3-D vessel geometry as well as cardiac dynamics, and propose a dynamic model based on the tracking of an elliptical vessel approximation to recover the rigid transformation and align IVUS images without loosing any IVUS data. We report an extensive validation with synthetic simulated data and in vivo IVUS sequences of 30 patients achieving an average reduction of the image artifact of 97% in synthetic data and 79% in real-data. Our study shows that IVUS alignment improves longitudinal analysis of the IVUS data and is a necessary step towards accurate reconstruction and volumetric measurements of 3-D IVUS.
Keywords: Intravascular ultrasound (IVUS); Motion estimation; Motion decomposition; Fourier
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Misael Rosales, Petia Radeva, Oriol Rodriguez, & Debora Gil. (2005). Suppression of IVUS Image Rotation. A Kinematic Approach. In Monica Andres and Hernandez Petia and Santos A. and R. Frangi (Ed.), Functional Imaging and Modeling of the Heart (Vol. 3504, pp. 889–892). LNCS, 3504. Springer Berlin / Heidelberg.
Abstract: IntraVascular Ultrasound (IVUS) is an exploratory technique used in interventional procedures that shows cross section images of arteries and provides qualitative information about the causes and severity of the arterial lumen narrowing. Cross section analysis as well as visualization of plaque extension in a vessel segment during the catheter imaging pullback are the technique main advantages. However, IVUS sequence exhibits a periodic rotation artifact that makes difficult the longitudinal lesion inspection and hinders any segmentation algorithm. In this paper we propose a new kinematic method to estimate and remove the image rotation of IVUS images sequences. Results on several IVUS sequences show good results and prompt some of the clinical applications to vessel dynamics study, and relation to vessel pathology.
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Mohamed Ali Souibgui. (2022). Document Image Enhancement and Recognition in Low Resource Scenarios: Application to Ciphers and Handwritten Text (Alicia Fornes, & Yousri Kessentini, Eds.). Ph.D. thesis, IMPRIMA, .
Abstract: In this thesis, we propose different contributions with the goal of enhancing and recognizing historical handwritten document images, especially the ones with rare scripts, such as cipher documents.
In the first part, some effective end-to-end models for Document Image Enhancement (DIE) using deep learning models were presented. First, Generative Adversarial Networks (cGAN) for different tasks (document clean-up, binarization, deblurring, and watermark removal) were explored. Next, we further improve the results by recovering the degraded document images into a clean and readable form by integrating a text recognizer into the cGAN model to promote the generated document image to be more readable. Afterward, we present a new encoder-decoder architecture based on vision transformers to enhance both machine-printed and handwritten document images, in an end-to-end fashion.
The second part of the thesis addresses Handwritten Text Recognition (HTR) in low resource scenarios, i.e. when only few labeled training data is available. We propose novel methods for recognizing ciphers with rare scripts. First, a few-shot object detection based method was proposed. Then, we incorporate a progressive learning strategy that automatically assignspseudo-labels to a set of unlabeled data to reduce the human labor of annotating few pages while maintaining the good performance of the model. Secondly, a data generation technique based on Bayesian Program Learning (BPL) is proposed to overcome the lack of data in such rare scripts. Thirdly, we propose a Text-Degradation Invariant Auto Encoder (Text-DIAE). This latter self-supervised model is designed to tackle two tasks, text recognition and document image enhancement. The proposed model does not exhibit limitations of previous state-of-the-art methods based on contrastive losses, while at the same time, it requires substantially fewer data samples to converge.
In the third part of the thesis, we analyze, from the user perspective, the usage of HTR systems in low resource scenarios. This contrasts with the usual research on HTR, which often focuses on technical aspects only and rarely devotes efforts on implementing software tools for scholars in Humanities.
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Mohamed Ali Souibgui, Ali Furkan Biten, Sounak Dey, Alicia Fornes, Yousri Kessentini, Lluis Gomez, et al. (2022). One-shot Compositional Data Generation for Low Resource Handwritten Text Recognition. In Winter Conference on Applications of Computer Vision.
Abstract: Low resource Handwritten Text Recognition (HTR) is a hard problem due to the scarce annotated data and the very limited linguistic information (dictionaries and language models). This appears, for example, in the case of historical ciphered manuscripts, which are usually written with invented alphabets to hide the content. Thus, in this paper we address this problem through a data generation technique based on Bayesian Program Learning (BPL). Contrary to traditional generation approaches, which require a huge amount of annotated images, our method is able to generate human-like handwriting using only one sample of each symbol from the desired alphabet. After generating symbols, we create synthetic lines to train state-of-the-art HTR architectures in a segmentation free fashion. Quantitative and qualitative analyses were carried out and confirm the effectiveness of the proposed method, achieving competitive results compared to the usage of real annotated data.
Keywords: Document Analysis
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Mohamed Ali Souibgui, Alicia Fornes, Y.Kessentini, & C.Tudor. (2021). A Few-shot Learning Approach for Historical Encoded Manuscript Recognition. In 25th International Conference on Pattern Recognition (pp. 5413–5420).
Abstract: Encoded (or ciphered) manuscripts are a special type of historical documents that contain encrypted text. The automatic recognition of this kind of documents is challenging because: 1) the cipher alphabet changes from one document to another, 2) there is a lack of annotated corpus for training and 3) touching symbols make the symbol segmentation difficult and complex. To overcome these difficulties, we propose a novel method for handwritten ciphers recognition based on few-shot object detection. Our method first detects all symbols of a given alphabet in a line image, and then a decoding step maps the symbol similarity scores to the final sequence of transcribed symbols. By training on synthetic data, we show that the proposed architecture is able to recognize handwritten ciphers with unseen alphabets. In addition, if few labeled pages with the same alphabet are used for fine tuning, our method surpasses existing unsupervised and supervised HTR methods for ciphers recognition.
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Mohamed Ali Souibgui, Alicia Fornes, Yousri Kessentini, & Beata Megyesi. (2022). Few shots are all you need: A progressive learning approach for low resource handwritten text recognition. PRL - Pattern Recognition Letters, 160, 43–49.
Abstract: Handwritten text recognition in low resource scenarios, such as manuscripts with rare alphabets, is a challenging problem. In this paper, we propose a few-shot learning-based handwriting recognition approach that significantly reduces the human annotation process, by requiring only a few images of each alphabet symbols. The method consists of detecting all the symbols of a given alphabet in a textline image and decoding the obtained similarity scores to the final sequence of transcribed symbols. Our model is first pretrained on synthetic line images generated from an alphabet, which could differ from the alphabet of the target domain. A second training step is then applied to reduce the gap between the source and the target data. Since this retraining would require annotation of thousands of handwritten symbols together with their bounding boxes, we propose to avoid such human effort through an unsupervised progressive learning approach that automatically assigns pseudo-labels to the unlabeled data. The evaluation on different datasets shows that our model can lead to competitive results with a significant reduction in human effort. The code will be publicly available in the following repository: https://github.com/dali92002/HTRbyMatching
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