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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
Kevin W. Eliceiri ( ) Corresponding author: email@example.com 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
Paddock and Kevin W. Eliceiri ... Fiji "Wellcome Trust Microscopy Resource" http://www.well.ox.ac.uk/external-website-links "Nikon Small World" http://www.nikonsmallworld.com/ "Olympus BioScapes" http://www.olympusbioscapes.com/ Stephen W. ...doi:10.1007/978-1-60761-847-8_2 pmid:24052346 fatcat:wrz4bgh5ojfvloglffhzyaencq
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
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
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 adoi:10.1091/mbc.e16-04-0223 pmid:27226483 pmcid:PMC4945144 fatcat:xh2pvogmxzfipp7kygr3q3hnsi
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
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 adoi:10.1101/2020.08.04.236364 fatcat:mbxavicqhrej3p7h3aneiyet4i
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.
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. Adoi:10.2144/01314bt01 pmid:11680704 fatcat:ia6jggueabh6nps5epfybmzeuu
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 isdoi:10.1146/annurev.biophys.050708.133641 pmid:19416072 pmcid:PMC3522875 fatcat:tslfmfzsdnb3xdgr5lx4btgjaa
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.
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 (http://imagej.net/ Downloads). Installation and use instructions available at http://imagej.net/MATLAB_Scripting. 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
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 isdoi:10.1016/j.tcb.2009.08.007 pmid:19833518 pmcid:PMC2789254 fatcat:ypmthppecrfylmwx5dzs6k2yp4
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.
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
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
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 scientificdoi:10.1186/s12859-016-1383-0 pmid:27927161 pmcid:PMC5142403 fatcat:h426vct23fbo3iroqffmn3yome
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.
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