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Dual-stream Maximum Self-attention Multi-instance Learning [article]

Bin Li, Kevin W. Eliceiri
2020 arXiv   pre-print
q h i , v i = W v h i , i = 0, . . . , N − 1 (4) Where W q and W v are weight matrices of two fully connected layers.  ...  The bag score c ∈ R C×1 is then given by: c b = W 1 b (7) Where W 1 is a weight matrix of a fully connected layer.  ... 
arXiv:2006.05538v1 fatcat:kggll3ztfjgj7mi7d24d5ethuq

Sonification of hyperspectral fluorescence microscopy datasets

Aprameya Mysore, Andreas Velten, Kevin W. Eliceiri
2016 F1000Research  
Kevin W. Eliceiri ( ) Corresponding author: Mysore A, Velten A and Eliceiri KW.  ...  Kevin Eliceiri initiated and oversaw the project. Data and software availability Competing interests No competing interests were disclosed.  ...  Mysore A, Velten A, Eliceiri KW: Sonification of focalcheck beads. Figshare. 2016. Data Source 32. Mysore A, Velten A, Eliceiri KW: Sonification of Arabidopsis Plastid and Cell Membrane.  ... 
doi:10.12688/f1000research.9233.1 fatcat:45ljsu7uzbgqvpw3h53aok544e

Laser Scanning Confocal Microscopy: History, Applications, and Related Optical Sectioning Techniques [chapter]

Stephen W. Paddock, Kevin W. Eliceiri
2013 Msphere  
Paddock and Kevin W. Eliceiri  ...  Fiji "Wellcome Trust Microscopy Resource" "Nikon Small World" "Olympus BioScapes" Stephen W.  ... 
doi:10.1007/978-1-60761-847-8_2 pmid:24052346 fatcat:wrz4bgh5ojfvloglffhzyaencq

Visualization approaches for multidimensional biological image data

Curtis T. Rueden, Kevin W. Eliceiri
2007 BioTechniques  
Rueden and Kevin W.  ...  Eliceiri The great advances in computing in recent years have allowed for the increased development of advanced multidimensional microscopy approaches by allowing for improved acquisition capabilities,  ... 
doi:10.2144/000112511 pmid:17936940 fatcat:khpxqyb275cfrkm3it6ld3t53y

A call for bioimaging software usability

Anne E Carpenter, Lee Kamentsky, Kevin W Eliceiri
2012 Nature Methods  
Bioimaging software developed in a research setting often fails to be widely used by the scientific community. We suggest that, to maximize both the public's and researchers' investments, usability should be a more highly valued goal. We describe specific characteristics of usability towards which bioimaging software projects should aim.
doi:10.1038/nmeth.2073 pmid:22743771 pmcid:PMC3641581 fatcat:7scliwbzjvddpiozd2m376ehsy

Membrane dynamics during cellular wound repair

Nicholas R. Davenport, Kevin J. Sonnemann, Kevin W. Eliceiri, William M. Bement, David G. Drubin
2016 Molecular Biology of the Cell  
Cells rapidly reseal after damage, but how they do so is unknown. It has been hypothesized that resealing occurs due to formation of a patch derived from rapid fusion of intracellular compartments at the wound site. However, patching has never been directly visualized. Here we study membrane dynamics in wounded Xenopus laevis oocytes at high spatiotemporal resolution. Consistent with the patch hypothesis, we find that damage triggers rampant fusion of intracellular compartments, generating a
more » ... rier that limits influx of extracellular dextrans. Patch formation is accompanied by compound exocytosis, local accumulation and aggregation of vesicles, and rupture of compartments facing the external environment. Subcellular patterning is evident as annexin A1, dysferlin, diacylglycerol, active Rho, and active Cdc42 are recruited to compartments confined to different regions around the wound. We also find that a ring of elevated intracellular calcium overlaps the region where membrane dynamics are most evident and persists for several minutes. The results provide the first direct visualization of membrane patching during membrane repair, reveal novel features of the repair process, and show that a remarkable degree of spatial patterning accompanies damage-induced membrane dynamics. Monitoring Editor
doi:10.1091/mbc.e16-04-0223 pmid:27226483 pmcid:PMC4945144 fatcat:xh2pvogmxzfipp7kygr3q3hnsi

Transient Room Lighting for Ambient Light Multiphoton Microscopy [article]

Andreas Velten, Adam J Uselmann, Surendra Prajapati, Jeremy S Bredfeldt, Thomas R Mackie, Kevin W Eliceiri
2020 bioRxiv   pre-print
Laser scanning microscopy techniques such as confocal and multiphoton fluorescence microscopy have been widely adopted by the biological research community due to their ability to monitor intact specimens at high spatial and temporal resolution. However, they have been limited for many biomedical, clinical and industrial applications by their fundamental need to operate in near absolute darkness. We present a lighting system that allows the use of light-sensitive imaging techniques in a
more » ... t room by interleaving capture and illumination at a high frequency and exploiting the light averaging properties of the human eye. We use this system with a multiphoton fluorescence microscope to illustrate that this method is capable of image capture in a well-lit room on par with capture in absolute darkness. This comparison is quantified through noise analysis of the images. This system has been implemented for laser scanning microscopy but has potential for widefield fluorescence imaging suitable for open-field surgery.
doi:10.1101/2020.08.04.236364 fatcat:mbxavicqhrej3p7h3aneiyet4i

LOCal: A Flexible Web-Based Microscope Reservation System

Kevin W. Eliceiri, Vincent P. Chu, John G. White
2001 BioTechniques  
Many microscopes, especially confocal and electron microscopes, are costly to purchase and maintain and are often only available in centralized facilities. The Internet has provided the potential for real-time accessibility to these microscopy resources with HTML pages describing the facility and the equipment available and, in some cases, the remote use of the microscope itself. Web-based booking systems have become another powerful way to improve accessibility to a microscope. A
more » ... calendar-based booking system for the online scheduling and user management of microscopes in laboratories and multi-user microscopy facilities is described. One extremely powerful application of Internet technology has been for individual research laboratories to create an online presence through the Web. Establishing such a Web presence has been facilitated by the advent of "what you see is what you get" HTML editors and easy-to-use Web server applications. The vast majority of laboratories now have Web sites that provide information about the laboratory, such as research projects, favorite protocols, and access to publications, images, and movies. Reflecting a trend seen in the general commodity Internet, these scientific sites have now become more sophisticated, often containing interactive content such as forms and Web databases. These interactive elements are created with "Internet-aware" scripting languages such as Perl, PHP, and JavaScript. The use of these scripting languages is not new. Perl, for example, has been used for Webbased input forms for years. However, as these scripting languages have become more powerful, so has their potential. About five years ago, we developed a Web calendar system for microscopes at the University of Wisconsin. Originally, we set out to provide a simple, no-frills, "paper calendar" system that would operate exactly like a paper calendar hanging on the door of a laboratory, except this would be modifiable and readable from a Web browser. As users and laboratory managers became accustomed to this simple system, we added new features such as user accounts, simple billing from the calendar, and the implementation of microscope usage rules in the calendar, such as hours of allowable use for different classes of user competencies. As the system became more complex and the underlying code more unwieldy, we decided to write a new purpose-built scheduling application for microscopy, rather than continuing to modify simple text-based or "flat file"-based systems. We have used the Web scripting language PHP and the database system MySQL to create a booking calendar system for microscopes. The speed and flexibility of these Web scripting languages has led to them being used extensively over the last 10 years for the creation of reservation calendars. Commonly used for booking lecture halls or announcing such events as 760BioTechniques Vol. 31, No.4 (2001) B iImaging Figure 1 . User modification window. This window allows the administrator to not only view all active users of a microscope but also to easily update and change their contact information and permissions. It also allows the administrator to assign users a temporary password if they forget their original one and to delete user accounts for former or suspended users.
doi:10.2144/01314bt01 pmid:11680704 fatcat:ia6jggueabh6nps5epfybmzeuu

Bioimage Informatics for Experimental Biology

Jason R. Swedlow, Ilya G. Goldberg, Kevin W. Eliceiri
2009 Annual Review of Biophysics  
Over the last twenty years there have been great advances in light microscopy with the result that multi-dimensional imaging has driven a revolution in modern biology. The development of new approaches of data acquisition are reportedly frequently, and yet the significant data management and analysis challenges presented by these new complex datasets remains largely unsolved. Like the well-developed field of genome bioinformatics, central repositories are and will be key resources, but there is
more » ... a critical need for informatics tools in individual laboratories to help manage, share, visualize, and analyze image data. In this article we present the recent efforts by the bioimage informatics community to tackle these challenges and discuss our own vision for future development of bioimage informatics solution. Experimental imaging data is by its very nature heterogeneous and dynamic. The challenge is to capture the evolving nature of an experiment in data structures that by their very nature are specifically typed and static, for later recall, analysis, and comparison. Achieving this goal in imaging applications means solving a number of problems: Proprietary file formats There are over 50 different proprietary file formats used in commercial and academic image acquisition software packages for light microscopy (36). This number only increases if electron microscopy, new HCS systems, tissue imaging systems and other new modes of imaging modalities are included. Regardless of the specific application, almost all store data in their own proprietary file format (PFFs). Each of these formats includes the binary data-the values in the pixels--and the metadata--the data that describes the binary data. Metadata includes physical pixel sizes, time stamps, spectral ranges, and any other measurements or Swedlow et al.
doi:10.1146/annurev.biophys.050708.133641 pmid:19416072 pmcid:PMC3522875 fatcat:tslfmfzsdnb3xdgr5lx4btgjaa

ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability

Mark C. Hiner, Curtis T. Rueden, Kevin W. Eliceiri
2016 Bioinformatics  
ImageJ-MATLAB is a lightweight Java library facilitating bi-directional interoperability between MATLAB and ImageJ. By defining a standard for translation between matrix and image data structures, researchers are empowered to select the best tool for their image-analysis tasks. Availability and Implementation: Freely available extension to ImageJ2 ( Downloads). Installation and use instructions available at Tested with ImageJ 2.0.0-rc-54, Java 1.8.0_66 and MATLAB R2015b.
doi:10.1093/bioinformatics/btw681 pmid:27797782 pmcid:PMC6041959 fatcat:ylxricb7jzgfvoijrfnacfmyqq

Open source bioimage informatics for cell biology

Jason R. Swedlow, Kevin W. Eliceiri
2009 Trends in Cell Biology  
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is
more » ... tated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery.
doi:10.1016/j.tcb.2009.08.007 pmid:19833518 pmcid:PMC2789254 fatcat:ypmthppecrfylmwx5dzs6k2yp4

Hyperdimensional Imaging Contrast Using an Optical Fiber

Jenu V. Chacko, Han Nim Lee, Wenxin Wu, Marisa S. Otegui, Kevin W. Eliceiri
2021 Sensors  
Seedlings were grown in mAIC (modified anthocyanin inductive condition) containing half-strength liquid Murashige and Skoog medium supplemented with 5% [w/v] sucrose on a rotary shaker with constant light  ...  Seedlings were grown in mAIC (modified anthocyanin inductive condition) containing half-strength liquid Murashige and Skoog medium supplemented with 5% [w/v] sucrose on a rotary shaker with constant light  ... 
doi:10.3390/s21041201 pmid:33572130 fatcat:g6w2cuccybewboj4jgs5tkn7vi

Applications of combined spectral lifetime microscopy for biology

Long Yan, Curtis T. Rueden, John G. White, Kevin W. Eliceiri
2006 BioTechniques  
doi:10.2144/000112251 pmid:16989084 fatcat:vzxn2rbya5cizgaf4zlc5j5sqi

2020 BioImage Analysis Survey: Community experiences and needs for the future [article]

Nasim Jamali, Ellen TA Dobson, Kevin W Eliceiri, Anne E. Carpenter, Beth A. Cimini
2021 bioRxiv   pre-print
We thank the members of the Eliceiri, Carpenter-Singh, and Cimini labs for their input on the questionnaire and assessment of needs in the bioimaging community.  ... 
doi:10.1101/2021.08.16.456498 fatcat:m2744l7b5jhatkkkvvfvgpijfy

SCIFIO: an extensible framework to support scientific image formats

Mark C. Hiner, Curtis T. Rueden, Kevin W. Eliceiri
2016 BMC Bioinformatics  
No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific
more » ... munity was lacking a domain-independent framework for format translation. Results: SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. Conclusions: SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.
doi:10.1186/s12859-016-1383-0 pmid:27927161 pmcid:PMC5142403 fatcat:h426vct23fbo3iroqffmn3yome
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