LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 53

Search options

  1. Book ; Online ; Thesis: Scalable image analysis for quantitative microscopy

    Preußer, Friedrich [Verfasser] / Rajewsky, Nikolaus [Gutachter] / Preibisch, Stephan [Gutachter] / Reber, Simone [Gutachter]

    2024  

    Author's details Friedrich Ludwig Preußer ; Gutachter: Nikolaus Rajewsky, Stephan Preibisch, Simone Reber
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Humboldt-Universität zu Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article: A scalable implementation of the recursive least-squares algorithm for training spiking neural networks.

    Arthur, Benjamin J / Kim, Christopher M / Chen, Susu / Preibisch, Stephan / Darshan, Ran

    Frontiers in neuroinformatics

    2023  Volume 17, Page(s) 1099510

    Abstract: Training spiking recurrent neural networks on neuronal recordings or behavioral tasks has become a popular way to study computations performed by the nervous system. As the size and complexity of neural recordings increase, there is a need for efficient ... ...

    Abstract Training spiking recurrent neural networks on neuronal recordings or behavioral tasks has become a popular way to study computations performed by the nervous system. As the size and complexity of neural recordings increase, there is a need for efficient algorithms that can train models in a short period of time using minimal resources. We present optimized CPU and GPU implementations of the recursive least-squares algorithm in spiking neural networks. The GPU implementation can train networks of one million neurons, with 100 million plastic synapses and a billion static synapses, about 1,000 times faster than an unoptimized reference CPU implementation. We demonstrate the code's utility by training a network, in less than an hour, to reproduce the activity of > 66, 000 recorded neurons of a mouse performing a decision-making task. The fast implementation enables a more interactive
    Language English
    Publishing date 2023-06-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2452979-5
    ISSN 1662-5196
    ISSN 1662-5196
    DOI 10.3389/fninf.2023.1099510
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.

    Preusser, Friedrich / Neuschulz, Anika / Junker, Jan Philipp / Rajewsky, Nikolaus / Preibisch, Stephan

    BMC biology

    2022  Volume 20, Issue 1, Page(s) 277

    Abstract: Background: During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to undergo adjustments at distinct temporal scales, from short-term dynamic changes in expression of ... ...

    Abstract Background: During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to undergo adjustments at distinct temporal scales, from short-term dynamic changes in expression of neurotransmitters and receptors to longer-term growth, spatial and connectivity reorganization, while integrating external stimuli. The nematode Caenorhabditis elegans provides a model of nervous system plasticity, in particular its dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive stress-resistant dauer stage and adapt their behavior to cope with the harsh new environment, with active reversal under improved conditions leading to resumption of reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larva's behavioral change is unknown. To fill this gap and provide insights on behavioral changes over extended periods of time, we developed a new open hardware method for long-term imaging (12h) of C. elegans larvae.
    Results: Our WormObserver platform comprises open hardware and software components for video acquisition, automated processing of large image data (> 80k images/experiment) and data analysis. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments and genetic backgrounds to identify key decision points and stimuli promoting dauer exit. Combining long-term behavioral imaging with transcriptomics data, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior.
    Conclusions: Taken together, we show how a developing nervous system can robustly integrate environmental changes activate a developmental switch and adapt the organism's behavior to a new environment. WormObserver is generally applicable to other research questions within and beyond the C. elegans field, having a modular and customizable character and allowing assessment of behavioral plasticity over longer periods.
    MeSH term(s) Animals ; Caenorhabditis elegans/physiology ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Larva ; Nematoda ; Neuropeptides/metabolism
    Chemical Substances Caenorhabditis elegans Proteins ; Neuropeptides
    Language English
    Publishing date 2022-12-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2133020-7
    ISSN 1741-7007 ; 1741-7007
    ISSN (online) 1741-7007
    ISSN 1741-7007
    DOI 10.1186/s12915-022-01471-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Book ; Online ; Thesis: Using modern microscopy and image analysis methods to study dosage compensation in C. elegans

    Breimann, Laura [Verfasser] / Pombo, Ana [Gutachter] / Preibisch, Stephan [Gutachter] / Reber, Simone [Gutachter]

    2022  

    Author's details Laura Breimann ; Gutachter: Ana Pombo, Stephan Preibisch, Simone Reber
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Humboldt-Universität zu Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Cap-dependent translation initiation monitored in living cells.

    Gandin, Valentina / English, Brian P / Freeman, Melanie / Leroux, Louis-Philippe / Preibisch, Stephan / Walpita, Deepika / Jaramillo, Maritza / Singer, Robert H

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 6558

    Abstract: mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding ... ...

    Abstract mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5'cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.
    MeSH term(s) RNA, Messenger/metabolism ; Peptide Initiation Factors/genetics ; Protein Biosynthesis ; RNA Caps/metabolism ; Peptide Chain Initiation, Translational
    Chemical Substances RNA, Messenger ; Peptide Initiation Factors ; RNA Caps
    Language English
    Publishing date 2022-11-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-34052-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Book ; Thesis: Reconstruction of multi-view microscopic acquisitions

    Preibisch, Stephan

    2011  

    Author's details von Stephan Preibisch
    Language English
    Size 135 S., Ill., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Techn. Univ., Diss.--Dresden, 2011
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Book ; Online: Software for Microscopy Workshop White Paper

    Chhetri, Raghav / Preibisch, Stephan / Stuurman, Nico

    2020  

    Abstract: Microscopes have morphed from purely optical instruments into motorized, robotic machines that form images on digital sensors rather than eyeballs. This continuing trend towards automation and digitization enables many new approaches to microscopy that ... ...

    Abstract Microscopes have morphed from purely optical instruments into motorized, robotic machines that form images on digital sensors rather than eyeballs. This continuing trend towards automation and digitization enables many new approaches to microscopy that would have been impossible or impractical without computer interfaces. Accordingly, todays development of new microscopes most often depends on concurrent software development to bring these custom-build systems to life. This dependence on software brings opportunities and challenges. Most importantly, a key challenge while developing new microscopes is to develop the appropriate software. Despite the fact that software is easily copied and distributed, remarkably few opportunities are available to share experiences creating microscope control software. In turn, this brings challenges in creating maintainable and flexible software code and writing User Interfaces (UIs) that are easily used by researchers, who are primarily life scientists. To start to address these challenges by identifying common problems and shared solutions, we assembled a small group of researchers that develop or use software to control their custom-build microscopes at the Janelia Research Campus for a two-day workshop in February 2020. The outcome of the workshop was the definition of clear milestones, as well as the recognition of an involved community, much larger than the one assembled at the workshop. This community encounters similar hurdles and shares a great desire to overcome these by stronger, community-wide collaborations on Open Source Software. This White Paper summarizes the major issues identified, proposes approaches to address these as a community, and outlines the next steps that can be taken to develop a framework facilitating shared microscope software development, significantly speeding up development of new microscopy systems.

    Comment: 10 pages
    Keywords Quantitative Biology - Other Quantitative Biology
    Subject code 303 ; 028
    Publishing date 2020-04-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Book ; Online: Tracking by weakly-supervised learning and graph optimization for whole-embryo C. elegans lineages

    Hirsch, Peter / Malin-Mayor, Caroline / Santella, Anthony / Preibisch, Stephan / Kainmueller, Dagmar / Funke, Jan

    2022  

    Abstract: Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point annotations with an ...

    Abstract Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point annotations with an integer linear program (ILP) for optimal cell lineage extraction. Our work specifically addresses the following challenging properties of C. elegans embryo recordings: (1) Many cell divisions as compared to benchmark recordings of other organisms, and (2) the presence of polar bodies that are easily mistaken as cell nuclei. To cope with (1), we devise and incorporate a learnt cell division detector. To cope with (2), we employ a learnt polar body detector. We further propose automated ILP weights tuning via a structured SVM, alleviating the need for tedious manual set-up of a respective grid search. Our method outperforms the previous leader of the cell tracking challenge on the Fluo-N3DH-CE embryo dataset. We report a further extensive quantitative evaluation on two more C. elegans datasets. We will make these datasets public to serve as an extended benchmark for future method development. Our results suggest considerable improvements yielded by our method, especially in terms of the correctness of division event detection and the number and length of fully correct track segments. Code: https://github.com/funkelab/linajea

    Comment: Accepted at MICCAI 2022, Code: https://github.com/funkelab/linajea
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning
    Subject code 006
    Publishing date 2022-08-24
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article: Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.

    Vladimirov, Nikita / Preusser, Friedrich / Wisniewski, Jan / Yaniv, Ziv / Desai, Ravi Anand / Woehler, Andrew / Preibisch, Stephan

    Biomedical optics express

    2021  Volume 12, Issue 4, Page(s) 2186–2203

    Abstract: Light-sheet microscopy has become indispensable for imaging developing organisms, and imaging from multiple directions (views) is essential to improve its spatial resolution. We combine multi-view light-sheet microscopy with microfluidics using adaptive ... ...

    Abstract Light-sheet microscopy has become indispensable for imaging developing organisms, and imaging from multiple directions (views) is essential to improve its spatial resolution. We combine multi-view light-sheet microscopy with microfluidics using adaptive optics (deformable mirror) which corrects aberrations introduced by the 45
    Language English
    Publishing date 2021-03-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2572216-5
    ISSN 2156-7085
    ISSN 2156-7085
    DOI 10.1364/BOE.416737
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.

    Preusser, Friedrich / Dos Santos, Natália / Contzen, Jörg / Stachelscheid, Harald / Costa, Érico Tosoni / Mergenthaler, Philipp / Preibisch, Stephan

    Bioinformatics (Oxford, England)

    2021  Volume 37, Issue 18, Page(s) 3088–3090

    Abstract: Summary: Here, we propose Fourier ring correlation-based quality estimation (FRC-QE) as a new metric for automated image quality estimation in 3D fluorescence microscopy acquisitions of cleared organoids that yields comparable measurements across ... ...

    Abstract Summary: Here, we propose Fourier ring correlation-based quality estimation (FRC-QE) as a new metric for automated image quality estimation in 3D fluorescence microscopy acquisitions of cleared organoids that yields comparable measurements across experimental replicates, clearing protocols and works for different microscopy modalities.
    Availability and implementation: FRC-QE is written in ImgLib2/Java and provided as an easy-to-use and macro-scriptable plugin for Fiji. Code, documentation, sample images and further information can be found under https://github.com/PreibischLab/FRC-QE.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Software ; Imaging, Three-Dimensional ; Microscopy, Fluorescence
    Language English
    Publishing date 2021-03-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btab160
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top