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  1. AU="Basurto-Lozada, Daniela"
  2. AU="Takashima, Shin-Ichiro"
  3. AU="Teresinha Leal"
  4. AU="Angélique B van 't Wout"
  5. AU="Roberts, Nicholas J"
  6. AU="Chauhan, Gaurav B"
  7. AU=Hanjaya-Putra Donny
  8. AU=Powell James
  9. AU="Russell, Todd"
  10. AU=Forth Scott
  11. AU="Kreutzer, Susanne" AU="Kreutzer, Susanne"
  12. AU="St John, Maie"
  13. AU=Gerhardy A
  14. AU="Qi, Huixin"
  15. AU="Dobosiewicz, May"
  16. AU="Srivastava, Rakesh"
  17. AU="Grevtsov K.I."

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  1. Artikel ; Online: Crop plot segmentation based on soil surface temperature dynamics

    Basurto-Lozada, Daniela / Salas, Joaquín / Acosta-Gallegos, Jorge Alberto

    Remote Sensing Applications: Society and Environment. 2023 Jan., v. 29 p.100871-

    2023  

    Abstract: The world’s growing population demands more food with high nutritious content, even though the agricultural fields are already under too much stress. This paper introduces a method for segmenting crop plots meaningful in terms of moisture availability ... ...

    Abstract The world’s growing population demands more food with high nutritious content, even though the agricultural fields are already under too much stress. This paper introduces a method for segmenting crop plots meaningful in terms of moisture availability for plant growth. In this approach, we characterize the dynamics of soil surface temperature of a fallow crop plot during the sunlight hours using UAS and reference values from i-buttons. Afterward, based on its characterization, we conduct an unsupervised clustering method to segment the plot area. Next, we employ machine learning methods to infer the soil classes at the early stages of crop growth at high resolution from UAS and lower resolution from multispectral satellite images. The neural network classifiers using data obtained with UAS have a ROC AUC above 0.67. The regressors using data from satellite imagery predict the percentage of pixels corresponding to soil classes with an RMSE below 0.17. The results show that the proposed methodology is sound and allows for surface clustering based on the dynamics of soil surface temperature.
    Schlagwörter environment ; plant growth ; remote sensing ; satellites ; soil ; solar radiation ; surface temperature ; Thermal remote sensing ; Soil surface temperature dynamics ; Machine learning for precision agriculture
    Sprache Englisch
    Erscheinungsverlauf 2023-01
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel ; Online
    ISSN 2352-9385
    DOI 10.1016/j.rsase.2022.100871
    Datenquelle NAL Katalog (AGRICOLA)

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  2. Artikel: OME-Zarr: a cloud-optimized bioimaging file format with international community support.

    Moore, Josh / Basurto-Lozada, Daniela / Besson, Sébastien / Bogovic, John / Bragantini, Jordão / Brown, Eva M / Burel, Jean-Marie / Moreno, Xavier Casas / de Medeiros, Gustavo / Diel, Erin E / Gault, David / Ghosh, Satrajit S / Gold, Ilan / Halchenko, Yaroslav O / Hartley, Matthew / Horsfall, Dave / Keller, Mark S / Kittisopikul, Mark / Kovacs, Gabor /
    Yoldaş, Aybüke Küpcü / Kyoda, Koji / de la Villegeorges, Albane le Tournoulx / Li, Tong / Liberali, Prisca / Lindner, Dominik / Linkert, Melissa / Lüthi, Joel / Maitin-Shepard, Jeremy / Manz, Trevor / Marconato, Luca / McCormick, Matthew / Lange, Merlin / Mohamed, Khaled / Moore, William / Norlin, Nils / Ouyang, Wei / Özdemir, Bugra / Palla, Giovanni / Pape, Constantin / Pelkmans, Lucas / Pietzsch, Tobias / Preibisch, Stephan / Prete, Martin / Rzepka, Norman / Samee, Sameeul / Schaub, Nicholas / Sidky, Hythem / Solak, Ahmet Can / Stirling, David R / Striebel, Jonathan / Tischer, Christian / Toloudis, Daniel / Virshup, Isaac / Walczysko, Petr / Watson, Alan M / Weisbart, Erin / Wong, Frances / Yamauchi, Kevin A / Bayraktar, Omer / Cimini, Beth A / Gehlenborg, Nils / Haniffa, Muzlifah / Hotaling, Nathan / Onami, Shuichi / Royer, Loic A / Saalfeld, Stephan / Stegle, Oliver / Theis, Fabian J / Swedlow, Jason R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing ...

    Abstract A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.
    Sprache Englisch
    Erscheinungsdatum 2023-05-07
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.02.17.528834
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Yolk sac cell atlas reveals multiorgan functions during human early development.

    Goh, Issac / Botting, Rachel A / Rose, Antony / Webb, Simone / Engelbert, Justin / Gitton, Yorick / Stephenson, Emily / Quiroga Londoño, Mariana / Mather, Michael / Mende, Nicole / Imaz-Rosshandler, Ivan / Yang, Lu / Horsfall, Dave / Basurto-Lozada, Daniela / Chipampe, Nana-Jane / Rook, Victoria / Lee, Jimmy Tsz Hang / Ton, Mai-Linh / Keitley, Daniel /
    Mazin, Pavel / Vijayabaskar, M S / Hannah, Rebecca / Gambardella, Laure / Green, Kile / Ballereau, Stephane / Inoue, Megumi / Tuck, Elizabeth / Lorenzi, Valentina / Kwakwa, Kwasi / Alsinet, Clara / Olabi, Bayanne / Miah, Mohi / Admane, Chloe / Popescu, Dorin-Mirel / Acres, Meghan / Dixon, David / Ness, Thomas / Coulthard, Rowen / Lisgo, Steven / Henderson, Deborah J / Dann, Emma / Suo, Chenqu / Kinston, Sarah J / Park, Jong-Eun / Polanski, Krzysztof / Marioni, John / van Dongen, Stijn / Meyer, Kerstin B / de Bruijn, Marella / Palis, James / Behjati, Sam / Laurenti, Elisa / Wilson, Nicola K / Vento-Tormo, Roser / Chédotal, Alain / Bayraktar, Omer / Roberts, Irene / Jardine, Laura / Göttgens, Berthold / Teichmann, Sarah A / Haniffa, Muzlifah

    Science (New York, N.Y.)

    2023  Band 381, Heft 6659, Seite(n) eadd7564

    Abstract: The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by ...

    Abstract The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds.
    Mesh-Begriff(e) Female ; Humans ; Pregnancy ; Blood Coagulation/genetics ; Macrophages ; Yolk Sac/cytology ; Yolk Sac/metabolism ; Embryonic Development/genetics ; Atlases as Topic ; Gene Expression ; Gene Expression Profiling ; Hematopoiesis/genetics ; Liver/embryology
    Sprache Englisch
    Erscheinungsdatum 2023-08-18
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.add7564
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: OME-Zarr: a cloud-optimized bioimaging file format with international community support.

    Moore, Josh / Basurto-Lozada, Daniela / Besson, Sébastien / Bogovic, John / Bragantini, Jordão / Brown, Eva M / Burel, Jean-Marie / Casas Moreno, Xavier / de Medeiros, Gustavo / Diel, Erin E / Gault, David / Ghosh, Satrajit S / Gold, Ilan / Halchenko, Yaroslav O / Hartley, Matthew / Horsfall, Dave / Keller, Mark S / Kittisopikul, Mark / Kovacs, Gabor /
    Küpcü Yoldaş, Aybüke / Kyoda, Koji / le Tournoulx de la Villegeorges, Albane / Li, Tong / Liberali, Prisca / Lindner, Dominik / Linkert, Melissa / Lüthi, Joel / Maitin-Shepard, Jeremy / Manz, Trevor / Marconato, Luca / McCormick, Matthew / Lange, Merlin / Mohamed, Khaled / Moore, William / Norlin, Nils / Ouyang, Wei / Özdemir, Bugra / Palla, Giovanni / Pape, Constantin / Pelkmans, Lucas / Pietzsch, Tobias / Preibisch, Stephan / Prete, Martin / Rzepka, Norman / Samee, Sameeul / Schaub, Nicholas / Sidky, Hythem / Solak, Ahmet Can / Stirling, David R / Striebel, Jonathan / Tischer, Christian / Toloudis, Daniel / Virshup, Isaac / Walczysko, Petr / Watson, Alan M / Weisbart, Erin / Wong, Frances / Yamauchi, Kevin A / Bayraktar, Omer / Cimini, Beth A / Gehlenborg, Nils / Haniffa, Muzlifah / Hotaling, Nathan / Onami, Shuichi / Royer, Loic A / Saalfeld, Stephan / Stegle, Oliver / Theis, Fabian J / Swedlow, Jason R

    Histochemistry and cell biology

    2023  Band 160, Heft 3, Seite(n) 223–251

    Abstract: A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing ...

    Abstract A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.
    Mesh-Begriff(e) Humans ; Software ; Microscopy ; Community Support
    Sprache Englisch
    Erscheinungsdatum 2023-07-10
    Erscheinungsland Germany
    Dokumenttyp Journal Article
    ZDB-ID 1222930-1
    ISSN 1432-119X ; 0301-5564 ; 0948-6143
    ISSN (online) 1432-119X
    ISSN 0301-5564 ; 0948-6143
    DOI 10.1007/s00418-023-02209-1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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