25 research outputs found
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services
Analyzing colony dynamics and visualizing cell diversity in spatiotemporal experiments
Hattab G. Analyzing colony dynamics and visualizing cell diversity in spatiotemporal experiments. Bielefeld: Universität Bielefeld; 2018.Bioimaging technologies enable the description of the life cycle of organisms at the microscopic scale, for example bacterial cells. In the particular case of time lapse imaging, the coupling of experimental setups and marker protocols results in the acquisition of biological changes in spatiotemporal experiments. Such experiments are devised to obtain a time-lapse image data, which I refer to as biomovies. Understanding how a cell behaves at every time point is crucial. In fact, this motivated all cell studies in the literature, which are single cell oriented. For the present biomovies, the task is to identify similarly fluorescing subpopulations across space and time.
My interest lies in isogenic bacterial populations of *Sinorhizobium meliloti*. The biomovies’ particularity is a dynamic range of high values for a set of different properties (e.g. cell density, cell count, etc), herein, leading to a bottleneck. State of the art methods cannot address such a task, which is partly due to their inability to handle highly dense populations and their adaptability to different experimental setups. In particular, they fall short either at the segmentation step (to delineate individual cells and extract their abstraction, e.g. cell centroid) or at the tracking step (to follow identified cells in each frame). To gain insight into bacterial growth at the population level, I claim that one does not really need to know the fate of each single cell.
In the context of this thesis, I present a series of pipelines and algorithms. First, preprocessing pipelines to reduce noise and enhance the object-to-background contrast. Second, an adaptive algorithm to correct spatial shift in the images (i.e. registration) and of each biomovie. Third and last, a modular algorithm that constructs coherent patch lineages by employing two adapted data abstractions, the particle and the patch, that are essential to solving the aforementioned bottleneck and are defined as follows: A particle is an intuitive geometric abstraction that results from considering whether the neighborhood around a pixel falls within a cell by checking for signal characteristics such as signal intensity, edge orientation, fluorescence signals, or texture. A patch is the aggregation of spatially contiguous particle trajectories that feature similar fluorescence patterns.
The methodology that creates coherent patch lineages is automatic and modular. By integrating aspects of object recognition and spatiotemporal changes, it lays down the foundation for investigating colony growth. All of the aforementioned pipelines represent a new methodological contribution to the field of lineage analysis and colony growth. I evaluate the proposed pipelines and algorithms on simulated and biological data, respectively. In turn this enabled me to validate the algorithms, interpret changes in the colony growth and differences among conditions of an experiment. In particular, I found that in a same condition, two isogenic bacterial colonies grew differently when faced with the same stress. The methods pioneered herein provide a key step to investigating colony growth
Leveraging Spatiotemporal Relationships of High-frequency Activation in Human Electrocorticographic Recordings for Speech Brain-Computer-Interface
Speech production is one of the most intricate yet natural human behaviors and is most keenly appreciated when it becomes difficult or impossible; as is the case for patients suffering from locked-in syndrome. Burgeoning understanding of the various cortical representations of language has brought into question the viability of a speech neuroprosthesis using implanted electrodes. The temporal resolution of intracranial electrophysiological recordings, frequently billed as a great asset of electrocorticography (ECoG), has actually been a hindrance as speech decoders have struggled to take advantage of this timing information. There have been few demonstrations of how well a speech neuroprosthesis will realistically generalize across contexts when constructed using causal feature extraction and language models that can be applied and adapted in real-time. The research detailed in this dissertation aims primarily to characterize the spatiotemporal relationships of high frequency activity across ECoG arrays during word production. Once identified, these relationships map to motor and semantic representations of speech through the use of algorithms and classifiers that rapidly quantify these relationships in single-trials. The primary hypothesis put forward by this dissertation is that the onset, duration and temporal profile of high frequency activity in ECoG recordings is a useful feature for speech decoding. These features have rarely been used in state-of-the-art speech decoders, which tend to produce output from instantaneous high frequency power across cortical sites, or rely upon precise behavioral time-locking to take advantage of high frequency activity at several time-points relative to behavioral onset times. This hypothesis was examined in three separate studies. First, software was created that rapidly characterizes spatiotemporal relationships of neural features. Second, semantic representations of speech were examined using these spatiotemporal features. Finally, utterances were discriminated in single-trials with low latency and high accuracy using spatiotemporal matched filters in a neural keyword-spotting paradigm. Outcomes from this dissertation inform implant placement for a human speech prosthesis and provide the scientific and methodological basis to motivate further research of an implant specifically for speech-based brain-computer-interfaces
Learning based biological image analysis
The fate of contemporary scientific research in biology and medicine is bound to the advancements in computational methods. The unprecedented data explosion in microscopy and the crescent interest of life scientists in studying more complex and more subtle interactions stimulate the research for innovative computational solutions on challenging real world applications. Extensions and novel formulations
of generic and flexible methods based on learning/inference are necessary to cope with the large variety of the produced data and to avoid continuous reimplementation
and heavy parameter tuning. This thesis exploits cutting edge machine learning methods based on structured probabilistic models and weakly supervised learning
to provide four novel solutions in the areas of large-scale microscopic imaging and multiple objects tracking.
Chapter 2 introduces a weakly supervised learning framework to tackle the problem of detecting defect images while mining massive microscopic imagery databases. This thesis demonstrates accurate prediction with low user annotation
effort. Chapter 3 presents a learning approach for counting overlapping objects in images based on local structured predictors. This problem has numerous applications
in high throughput microscopy screening such as cells counting for drug toxicity assays. Chapter 4 develops a deterministic graphical model to impose temporal consistency in objects counts when dealing with a video sequence. This Chapter shows that global (temporal and spatial) structural inference consistently
improves over local (only spatial) predictions. The method developed in Chapter 4 is used in a novel downstream tracking algorithm which is introduced in Chapter 5.
This Chapter tackles, for the first time, the difficult problem of tracking heavily overlapping, translucent and indistinguishable objects. The mutual occlusion event
handling of such objects is formulated as a novel structured inference problem based on the minimization of a convex multi-commodity flow energy. The optimal
weights of the energy terms are learned with partial user supervision using structured learning with latent variables.To support behavioral biologists, we apply this method to the problem of tracking a community of interacting Drosophila larvae
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services
A Review on Explainable Artificial Intelligence for Healthcare: Why, How, and When?
Artificial intelligence (AI) models are increasingly finding applications in
the field of medicine. Concerns have been raised about the explainability of
the decisions that are made by these AI models. In this article, we give a
systematic analysis of explainable artificial intelligence (XAI), with a
primary focus on models that are currently being used in the field of
healthcare. The literature search is conducted following the preferred
reporting items for systematic reviews and meta-analyses (PRISMA) standards for
relevant work published from 1 January 2012 to 02 February 2022. The review
analyzes the prevailing trends in XAI and lays out the major directions in
which research is headed. We investigate the why, how, and when of the uses of
these XAI models and their implications. We present a comprehensive examination
of XAI methodologies as well as an explanation of how a trustworthy AI can be
derived from describing AI models for healthcare fields. The discussion of this
work will contribute to the formalization of the XAI field.Comment: 15 pages, 3 figures, accepted for publication in the IEEE
Transactions on Artificial Intelligenc
Human-Centered Content-Based Image Retrieval
Retrieval of images that lack a (suitable) annotations cannot be achieved through (traditional) Information Retrieval (IR) techniques. Access through such collections can be achieved through the application of computer vision techniques on the IR problem, which is baptized Content-Based Image Retrieval (CBIR). In contrast with most purely technological approaches, the thesis Human-Centered Content-Based Image Retrieval approaches the problem from a human/user centered perspective. Psychophysical experiments were conducted in which people were asked to categorize colors. The data gathered from these experiments was fed to a Fast Exact Euclidean Distance (FEED) transform (Schouten & Van den Broek, 2004), which enabled the segmentation of color space based on human perception (Van den Broek et al., 2008). This unique color space segementation was exploited for texture analysis and image segmentation, and subsequently for full-featured CBIR. In addition, a unique CBIR-benchmark was developed (Van den Broek et al., 2004, 2005). This benchmark was used to explore what and how several parameters (e.g., color and distance measures) of the CBIR process influence retrieval results. In contrast with other research, users judgements were assigned as metric. The online IR and CBIR system Multimedia for Art Retrieval (M4ART) (URL: http://www.m4art.org) has been (partly) founded on the techniques discussed in this thesis. References: - Broek, E.L. van den, Kisters, P.M.F., and Vuurpijl, L.G. (2004). The utilization of human color categorization for content-based image retrieval. Proceedings of SPIE (Human Vision and Electronic Imaging), 5292, 351-362. [see also Chapter 7] - Broek, E.L. van den, Kisters, P.M.F., and Vuurpijl, L.G. (2005). Content-Based Image Retrieval Benchmarking: Utilizing Color Categories and Color Distributions. Journal of Imaging Science and Technology, 49(3), 293-301. [see also Chapter 8] - Broek, E.L. van den, Schouten, Th.E., and Kisters, P.M.F. (2008). Modeling Human Color Categorization. Pattern Recognition Letters, 29(8), 1136-1144. [see also Chapter 5] - Schouten, Th.E. and Broek, E.L. van den (2004). Fast Exact Euclidean Distance (FEED) transformation. In J. Kittler, M. Petrou, and M. Nixon (Eds.), Proceedings of the 17th IEEE International Conference on Pattern Recognition (ICPR 2004), Vol 3, p. 594-597. August 23-26, Cambridge - United Kingdom. [see also Appendix C
Computational Image Analysis For Axonal Transport, Phenotypic Profiling, And Digital Pathology
Recent advances in fluorescent probes, microscopy, and imaging platforms have revolutionized biology and medicine, generating multi-dimensional image datasets at unprecedented scales. Traditional, low-throughput methods of image analysis are inadequate to handle the increased “volume, velocity, and variety” that characterize the realm of big data. Thus, biomedical imaging requires a new set of tools, which include advanced computer vision and machine learning algorithms. In this work, we develop computational image analysis solutions to biological questions at the level of single-molecules, cells, and tissues. At the molecular level, we dissect the regulation of dynein-dynactin transport initiation using in vitro reconstitution, single-particle tracking, super-resolution microscopy, live-cell imaging in neurons, and computational modeling. We show that at least two mechanisms regulate dynein transport initiation neurons: (1) cytoplasmic linker proteins, which are regulated by phosphorylation, increase the capture radius around the microtubule, thus reducing the time cargo spends in a diffusive search; and (2) a spatial gradient of tyrosinated alpha-tubulin enriched in the distal axon increases the affinity of dynein-dynactin for microtubules. Together, these mechanisms support a multi-modal recruitment model where interacting layers of regulation provide efficient, robust, and spatiotemporal control of transport initiation. At the cellular level, we develop and train deep residual convolutional neural networks on a large and diverse set of cellular microscopy images. Then, we apply networks trained for one task as deep feature extractors for unsupervised phenotypic profiling in a different task. We show that neural networks trained on one dataset encode robust image phenotypes that are sufficient to cluster subcellular structures by type and separate drug compounds by the mechanism of action, without additional training, supporting the strength and flexibility of this approach. Future applications include phenotypic profiling in image-based screens, where clustering genetic or drug treatments by image phenotypes may reveal novel relationships among genetic or pharmacologic pathways. Finally, at the tissue level, we apply deep learning pipelines in digital pathology to segment cardiac tissue and classify clinical heart failure using whole-slide images of cardiac histopathology. Together, these results demonstrate the power and promise of computational image analysis, computer vision, and deep learning in biological image analysis