Edge adaptive filtering of depth maps for mobile devices

Abstract. Mobile phone cameras have an almost unlimited depth of field, and therefore the images captured with them have wide areas in focus. When the depth of field is digitally manipulated through image processing, accurate perception of depth in a captured scene is important. Capturing depth data requires advanced imaging methods. In case a stereo lens system is used, depth information is calculated from the disparities between stereo frames. The resulting depth map is often noisy or doesn’t have information for every pixel. Therefore it has to be filtered before it is used for emphasizing depth. Edges must be taken into account in this process to create natural-looking shallow depth of field images. In this study five filtering methods are compared with each other. The main focus is the Fast Bilateral Solver, because of its novelty and high reported quality. Mobile imaging requires fast filtering in uncontrolled environments, so optimizing the processing time of the filters is essential. In the evaluations the depth maps are filtered, and the quality and the speed is determined for every method. The results show that the Fast Bilateral Solver filters the depth maps well, and can handle noisy depth maps better than the other evaluated methods. However, in mobile imaging it is slow and needs further optimization.Reunatietoinen syvyyskarttojen suodatus mobiililaitteilla. Tiivistelmä. Matkapuhelimien kameroissa on lähes rajoittamaton syväterävyysalue, ja siksi niillä otetuissa kuvissa laajat alueet näkyvät tarkennettuina. Digitaalisessa syvyysterävyysalueen muokkauksessa tarvitaan luotettava syvyystieto. Syvyysdatan hankinta vaatii edistyneitä kuvausmenetelmiä. Käytettäessä stereokameroita syvyystieto lasketaan kuvien välisistä dispariteeteista. Tuloksena syntyvä syvyyskartta on usein kohinainen, tai se ei sisällä syvyystietoa joka pikselille. Tästä syystä se on suodatettava ennen käyttöä syvyyden korostamiseen. Tässä prosessissa reunat ovat otettava huomioon, jotta saadaan luotua luonnollisen näköisiä kapean syväterävyysalueen kuvia. Tässä tutkimuksessa verrataan viittä suodatusmenetelmää keskenään. Eniten keskitytään nopeaan bilateraaliseen ratkaisijaan, johtuen sen uutuudesta ja korkeasta tuloksen laadusta. Mobiililaitteella kuvantamisen vaatimuksena on nopea suodatus hallitsemattomissa olosuhteissa, joten suodattimien prosessointiajan optimointi on erittäin tärkeää. Vertailuissa syvyyskuvat suodatetaan ja suodatuksen laatu ja nopeus mitataan jokaiselle menetelmälle. Tulokset osoittavat, että nopea bilateraalinen ratkaisija suodattaa syvyyskarttoja hyvin ja osaa käsitellä kohinaisia syvyyskarttoja paremmin kuin muut tarkastellut menetelmät. Mobiilikuvantamiseen se on kuitenkin hidas ja tarvitsee pidemmälle menevää optimointia

Robust Framework For Digital Image Denoising And Deblurring

Image restoration concerns improving visual quality of a captured image that goes beyond the achievable limit of camera. Recent advancement in imaging and multimedia technology has advocated the interests of image restoration through software, of which applications permeate consumer photography as well as different industries. Unfortunately, the captured images often suffer from degradations, such as blurring, noise, unpleasant artifacts, and more, due to limitations of the imaging system. Despite considerable efforts have been channeled to advance the state-of-the-art methods, surprisingly, these methods are often slow and only designed for handling specific degradation model

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

BACKGROUND The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level. METHODS Human tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing. RESULTS The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference. CONCLUSION Given that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images