المؤلفون: Singh, Harbinder, Forero, Manuel G., Agaoglu, Nuray, Bueno, Gloria, Deniz, Oscar, Cristóbal, Gabriel

المساهمون: Junta de Comunidades de Castilla-La Mancha, Ministerio de Ciencia e Innovación (España)

مصطلحات موضوعية: Depth-of-field, Image fusion, Quality metrics, Noise, ImageJ, Edge-preserving filter (EPF), Preservation of details

الوصف: 13 pags., 4 figs., 2 tabs. -- Event: SPIE Photonics Europe, 2024, Strasbourg, France ; This work was partially funded by projects SBPLY/21/180501/000025 by the Autonomous Government of Castilla-La Mancha and TED2021-132147B-100 (funded by MCIN/AEI/10.13039/501100011033 and by the European Union NextGenerationEU/PRTR). ; Peer reviewed

العلاقة: #PLACEHOLDER_PARENT_METADATA_VALUE#; info:eu-repo/grantAgreement/MICIN//TED2021-132147B-100; Postprint; https://doi.org/10.1117/12.3017408Test; Sí; Proceedings of SPIE 12998 Optics, Photonics, and Digital Technologies for Imaging Applications VIII (2024); http://hdl.handle.net/10261/361518Test

الإتاحة: https://doi.org/10.1117/12.3017408Test
http://hdl.handle.net/10261/361518Test

المؤلفون: Nunes, Margarida, Martins, G. Wanzeller, Sarraguça, Jorge, Olival, Fernanda, Moita, Patrícia, Mitchell, Scott G., Claro, Ana, Ferreira, Teresa

المساهمون: Fundação para a Ciência e a Tecnologia (Portugal), Consejo Superior de Investigaciones Científicas (España)

مصطلحات موضوعية: Blotting sands, SEM-EDS, Vibrational spectroscopy, ImageJ®, Multivariate analysis

الوصف: Too little is known about areia de escrever, i.e., blotting sands, the intriguing particles sprinkled on freshly written scripts to accelerate the drying time of the ink. Blotting sands constitute a valuable but underestimated historical source. ; This work investigated the blotting sands used on the account books of the religious houses scattered across continental Portugal and Madeira Island (16th-19th centuries). The sands were mainly composed of different minerals, predominately black sands, but in a few cases, minerals were found mixed with gums, paper cocoons or bone shavings. The combined use of SEM-EDS, µ-Raman and FT-IR techniques uncovered the materials' chemical or mineralogical composition and morphology. This approach, allied with image analysis and statistics complemented with multivariate analysis, allowed us to look for trends between the samples and hypothesise about their provenance. Heavy minerals, such as ilmenite, hematite and almandine, were identified as major components, together with other silicates (e.g. quartz). Samples were dominated by medium-sized grains with shape features indicating texturally mature sediments resulting from a medium-to-long sedimentary transport. Due to shorter geological transport distances, Madeira Island was the exception, with more angular grains. This work allowed us to uncover blotting sands, value them as historical sources, and establish a roadmap for their use in Portugal, aiming to pave the way towards a more global context in Europe. ; The authors acknowledge the National Archive of Torre do Tombo (ANTT), National Library of Portugal (BNP) and Public Library of Évora (BPE) for providing access to the samples and FCT for funding (IronIC project PTDC/ART-HIS/32327/2017, UIDB/04449/2020, UIDP/04449/2020, and UIDB/00057/2020). M. Nunes thanks the support of the FCT for a PhD grant (SFRH/BD/147528/2019), and G. Wanzeller Martins also thanks FCT for the grant BI-PTDC/ART-HIS/32327/2017 in the scope of the IronIC project (http://ironic.fcsh.unl.ptTest/). The ...

وصف الملف: application/pdf

العلاقة: Publisher's version; The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI 10.1016/j.saa.2023.123204; https://doi.org/10.1016/j.saa.2023.123204Test; Sí; Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 303: 123204 (2023); http://hdl.handle.net/10261/344069Test

الإتاحة: https://doi.org/10.1016/j.saa.2023.123204Test
http://hdl.handle.net/10261/344069Test

المؤلفون: Nunes, Margarida, Martins, G. Wanzeller, Sarraguça, Jorge, Olival, Fernanda, Moita, Patrícia, Mitchell, Scott G., Claro, Ana, Ferreira, Teresa

المساهمون: Fundação para a Ciência e a Tecnologia (Portugal)

مصطلحات موضوعية: Blotting sands, Inquisitorial archives, ImageJ®, Chemometrics, SEM/EDS, Raman spectroscopy

الوصف: Historical and archival research focused on the Portuguese Inquisition documents (1551–1800) uncovered the use of arena known as blotting sands, a writing accessory used to hasten ink drying. We present in this work the first systematic study combining image analysis, SEM/EDS and µ-Raman techniques, statistics and chemometrics to characterise the blotting sands used by the Portuguese Inquisition and hypothesise their provenance. Iron-titanium and iron oxide minerals categorised as texturally mature sands are the dominant species, consistent with sediment extraction from fluvial or beach contexts and later processed. Chemometrics unveiled time period trends by clustering the samples according to morphology and composition data. This work constitutes a groundbreaking step towards uncovering this intricate writing tool. ; The authors acknowledge the ANTT team for providing access to the samples and FCT for funding (IronIC project PTDC/ART-HIS/32327/2017 and UIDB/04449/2020, UIDP/04449/2020, LA/P/0132/2020, UIDB/00057/2020 projects). M. Nunes and G. Wanzeller Martins thank the support of the FCT for the PhD grants (SFRH/BD/147528/2019 and BI_PTDC/ART-HIS/32327/2017, respectively). ; Peer reviewed

وصف الملف: application/pdf

العلاقة: Publisher's version; The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI 10.1016/j.culher.2023.04.003; https://doi.org/10.1016/j.culher.2023.04.003Test; Sí; Journal of Cultural Heritage 61: 211-216 (2023); http://hdl.handle.net/10261/343944Test

الإتاحة: https://doi.org/10.1016/j.culher.2023.04.003Test
http://hdl.handle.net/10261/343944Test

المؤلفون: Talayero, Vanessa C., Vicente-Manzanares, Miguel

المساهمون: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Asociación Española Contra el Cáncer, Junta de Castilla y León

مصطلحات موضوعية: Focal adhesion, Protrusion, Actin cytoskeleton, ImageJ

الوصف: Focal adhesions in planar substrates constitute an excellent cellular resource to evaluate different parameters related to cell morphology, cytoskeletal organization, and adhesive strength. However, their intrinsic heterogeneity in terms of size, molecular composition, orientation, and so on complicates their analysis. Here, we describe a simple and straightforward ImageJ/Fiji-based method to quantify several parameters that describe the morphology and relative composition of focal adhesions. This type of analysis can be implemented in various ways and become useful for drug and shRNA screenings. ; This work was funded by the Spanish Ministry of Science and Innovation (SAF2017-87408), AECC Seed award (2018–IDEAS18018VICE) and ECRIN_M3-2020 (Accelerator Award) from CRUK/AECC/AIRC. The host institution, IBMCC, is supported by the Programa de Apoyo a Planes Estratégicos de Investigación de Estructuras de Investigación de Excelencia of the Ministry of Education of the Castilla–León Government (CLC–2017–01).

العلاقة: #PLACEHOLDER_PARENT_METADATA_VALUE#; SAF2017-87408SAF2017-87408; SAF2017-87408/AEI/10.13039/501100011033; Postprint; http://dx.doi.org/10.1007/978-1-0716-0962-0_3Test; Sí; Methods in molecular biology (Clifton, N.J.) 2217: 27-37 (2020); http://hdl.handle.net/10261/234059Test; http://dx.doi.org/10.13039/501100011033Test; http://dx.doi.org/10.13039/501100014180Test

الإتاحة: https://doi.org/10.1007/978-1-0716-0962-0_3Test
https://doi.org/10.13039/501100011033Test
https://doi.org/10.13039/501100014180Test
http://hdl.handle.net/10261/234059Test

المؤلفون: Tosi, Sébastien, Bardia, Lídia, Barallobre, María-José, Muñoz-Barrutia, Arrate, Soto-Montenegro, María Luisa, Colombelli, Julien

المساهمون: Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Instituto de Salud Carlos III, Agencia Estatal de Investigación (España)

مصطلحات موضوعية: 3D stitching, Lightsheet microscopy, Tiled scan, Mosaic, ImageJ

الوصف: © 2020 Tosi S et al. ; We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, sample fiducials, or conversion of raw TIFF images, and the stitched images can be explored instantly. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-side lightsheet illumination and dual-side camera detection. ; The preparation of some of the datasets that were used to test MosaicExplorerJ was partially funded by project TEC2016-78052-R from the Spanish Ministry of Economy and Competitiveness and RTC2017-6600-1 from Ministry of Science, Innovation and Universities, as well as project PI17/01766 from Ministerio de Ciencia, Innovación y Universidades, Instituto de Salud Carlos III (co-financed by European Regional Development Fund (ERDF), “A way of making Europe").

العلاقة: #PLACEHOLDER_PARENT_METADATA_VALUE#; info:eu-repo/grantAgreement/MINECO//TEC2016-78052-R; info:eu-repo/grantAgreement/RTC2017-6600-1; Publisher's version; http://dx.doi.org/10.12688/F1000RESEARCH.27112.1Test; Sí; F1000Research 9: 1-15 (2021); http://hdl.handle.net/10261/259911Test; http://dx.doi.org/10.13039/501100011033Test; http://dx.doi.org/10.13039/501100004587Test; http://dx.doi.org/10.13039/501100003329Test

الإتاحة: https://doi.org/10.12688/F1000RESEARCH.27112.1Test
https://doi.org/10.13039/501100011033Test
https://doi.org/10.13039/501100004587Test
https://doi.org/10.13039/501100003329Test
http://hdl.handle.net/10261/259911Test

المؤلفون: Tosi, Sébastien, Bardia, Lídia, Barallobre, María-José, Muñoz-Barrutia, Arrate, Soto-Montenegro, María Luisa, Colombelli, Julien

المساهمون: European Cooperation in Science and Technology, Jérôme Lejeune Foundation, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Instituto de Salud Carlos III

مصطلحات موضوعية: 3D stitching, Lightsheet microscopy, Tiled scan, Mosaic, ImageJ

الوصف: © 2021 Tosi S et al. ; We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection. ; This publication was supported by COST Action NEUBIAS (CA15124), funded by COST (European Cooperation in Science and Technology). MJB acknowledges the support of Jérôme Lejeune Foundation. : The preparation of some of the datasets that were used to test MosaicExplorerJ was partially funded by project TEC2016-78052-R from the Spanish Ministry of Economy and Competitiveness and RTC2017-6600-1 from Ministry of Science, Innovation and Universities, as well as project PI17/01766 from Ministerio de Ciencia, Innovación y Universidades, Instituto de Salud Carlos III (cofinanced by European Regional Development Fund (ERDF), “A way of making Europe").

العلاقة: #PLACEHOLDER_PARENT_METADATA_VALUE#; info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/TEC2016-78052-R; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTC2017-6600-1; RTC2017-6600-1/AEI/10.13039/501100011033; Publisher's version; http://dx.doi.org/10.12688/f1000research.27112.2Test; Sí; F1000Research 9: 1308 L (2021); http://hdl.handle.net/10261/250659Test; http://dx.doi.org/10.13039/501100011033Test; http://dx.doi.org/10.13039/501100000921Test; http://dx.doi.org/10.13039/501100004587Test; http://dx.doi.org/10.13039/100007353Test; http://dx.doi.org/10.13039/501100003329Test

الإتاحة: https://doi.org/10.12688/f1000research.27112.2Test
https://doi.org/10.13039/501100011033Test
https://doi.org/10.13039/501100000921Test
https://doi.org/10.13039/501100004587Test
https://doi.org/10.13039/100007353Test
https://doi.org/10.13039/501100003329Test
http://hdl.handle.net/10261/250659Test

المؤلفون: Gallego-Sánchez, L., Canales, Francisco José, Montilla-Bascón, Gracia, Prats, Elena

المساهمون: Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission

مصطلحات موضوعية: Rust, Infection frequency, Disease severity, Image analysis, Fiji, ImageJ

الوصف: © 2020 by the authors. ; Recently, phenotyping has become one of the main bottlenecks in plant breeding and fundamental plant science. This is particularly true for plant disease assessment, which has to deal with time-consuming evaluations and the subjectivity of visual assessments. In this work, we have developed an open source Robust, User-friendy Script Tool (RUST) for semi-automated evaluation of leaf rust diseases. RUST runs under the free Fiji imaging software (developed from ImageJ), which is a well-recognized software among the scientific community. The script enables the evaluation of leaf rust diseases using a color transformation tool and provides three different automation modes. The script opens images sequentially and records infection frequency (pustules per area) (semi-)automatically for high-throughput analysis. Furthermore, it can manage several scanned leaf segments in the same image, consecutively selecting the desired segments. The script has been validated with nearly 900 samples from 80 oat genotypes ranging from resistant to susceptible and from very light to heavily infected leaves showing a high accuracy with a Lin’s concordance correlation coefficient of 0.99. The analysis show a high repeatability as indicated by the low variation coefficients obtained when repeating the measurement of the same samples. The script also has optional steps for calibration and training to ensure accuracy, even in low-resolution images. This script can evaluate efficiently hundreds of leaves facilitating the screening of novel sources of resistance to this important cereal disease. ; This research was funded by Spanish Ministry of Science and Innovation [PID2019-104518RB-I00], (AEI/FEDER, UE), regional government through the AGR-253 group, and the European Regional and Social Development Funds. LG is holder of a FPI fellowship from the Spanish Ministry of Science and Innovation [BES-2017-080152]. ; Peer reviewed

العلاقة: #PLACEHOLDER_PARENT_METADATA_VALUE#; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-104518RB-I00; PID2019-104518RB-I00/AEI/10.13039/501100011033; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/BES-2017-080152; BES-2017-080152/AEI/10.13039/501100011033; Publisher’s version; https://doi.org/10.3390/plants9091182Test; Sí; Plants 9(9): 1182 (2020); http://hdl.handle.net/10261/220335Test; http://dx.doi.org/10.13039/501100000780Test; http://dx.doi.org/10.13039/501100011033Test

الإتاحة: https://doi.org/10.3390/plants9091182Test
https://doi.org/10.13039/501100000780Test
https://doi.org/10.13039/501100011033Test
http://hdl.handle.net/10261/220335Test

المؤلفون: Pijuan, Jordi, Barceló, Carla, Moreno, David F., Maiques, Óscar, Sisó, Pol, Marti, Rosa M., Macià, Anna, Panosa, Anaïs

المساهمون: Instituto de Salud Carlos III, European Commission, Asociación Española Contra el Cáncer

مصطلحات موضوعية: Cell migration/invasion, Wound healing assay, Scratch assay, Transwell assay, Spreading assay, Live cell imaging, Data analysis, ImageJ/Fiji

الوصف: © 2019 Pijuan, Barceló, Moreno, Maiques, Sisó, Marti, Macià and Panosa. ; Cell migration is a key procedure involved in many biological processes including embryological development, tissue formation, immune defense or inflammation, and cancer progression. How physical, chemical, and molecular aspects can affect cell motility is a challenge to understand migratory cells behavior. In vitro assays are excellent approaches to extrapolate to in vivo situations and study live cells behavior. Here we present four in vitro protocols that describe step-by-step cell migration, invasion and adhesion strategies and their corresponding image data quantification. These current protocols are based on two-dimensional wound healing assays (comparing traditional pipette tip-scratch assay vs. culture insert assay), 2D individual cell-tracking experiments by live cell imaging and three-dimensional spreading and transwell assays. All together, they cover different phenotypes and hallmarks of cell motility and adhesion, providing orthogonal information that can be used either individually or collectively in many different experimental setups. These optimized protocols will facilitate physiological and cellular characterization of these processes, which may be used for fast screening of specific therapeutic cancer drugs for migratory function, novel strategies in cancer diagnosis, and for assaying new molecules involved in adhesion and invasion metastatic properties of cancer cells. ; This work was supported by grants from ISCIII/FEDER Una manera de hacer Europa (PI12/00260, PI15/00711 to RM and PI18/00573 to RM and AM) and CIBERONC. CB holds predoctoral fellowship from UdL-IRBLleida. AM holds postdoctoral fellowship from AECC.

العلاقة: Publisher's version; http://dx.doi.org/10.3389/fcell.2019.00107Test; Sí; Front Cell Dev Biol 7: 107 (2019); http://hdl.handle.net/10261/201565Test; http://dx.doi.org/10.13039/501100004587Test; http://dx.doi.org/10.13039/501100000780Test

الإتاحة: https://doi.org/10.3389/fcell.2019.00107Test
https://doi.org/10.13039/501100004587Test
https://doi.org/10.13039/501100000780Test
http://hdl.handle.net/10261/201565Test

المؤلفون: Diez-Hermano, Sergio, Valero, Jorge, Rueda, Cristina, Ganfornina, M. D., Sánchez, Diego

المساهمون: Consejo Superior de Investigaciones Científicas (España)

مصطلحات موضوعية: Eye classifier, ImageJ plugin, Neurodegeneration, Ommatidia

الوصف: This is an Open Access article distributed under the terms of the Creative Commons Attribution License. ; The fruitfly compound eye has been broadly used as a model for neurodegenerative diseases. Classical quantitative techniques to estimate the degeneration level of an eye under certain experimental conditions rely either on time consuming histological techniques to measure retinal thickness, or pseudopupil visualization and manual counting. Alternatively, visual examination of the eye surface appearance gives only a qualitative approximation provided the observer is well-trained. Therefore, there is a need for a simplified and standardized analysis of fruitfly eye degeneration extent for both routine laboratory use and for automated high-throughput analysis. We have designed the freely available ImageJ plugin FLEYE, a novel and user-friendly method for quantitative unbiased evaluation of neurodegeneration levels based on the acquisition of fly eye surface pictures. The incorporation of automated image analysis tools and a classification algorithm sustained on a built-in statistical model allow the user to quickly analyze large sample size data with reliability and robustness. Pharmacological screenings or genetic studies using the Drosophila retina as a model system may benefit from our method, because it can be easily implemented in a fully automated environment. In addition, FLEYE can be trained to optimize the image detection capabilities, resulting in a versatile approach to evaluate the pattern regularity of other biological or non-biological samples and their experimental or pathological disruption. ; We acknowledge the support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI). ; Peer reviewed

العلاقة: Publisher's version; http://dx.doi.org/10.1186/s13024-015-0005-zTest; Sí; Molecular Neurodegeneration 10: 9 (2015); http://hdl.handle.net/10261/122806Test; http://dx.doi.org/10.13039/501100003339Test

الإتاحة: https://doi.org/10.1186/s13024-015-0005-zTest
https://doi.org/10.13039/501100003339Test
http://hdl.handle.net/10261/122806Test