Vineside - a microscopy dataset of grapevine wood anatomy over 6 months
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| Format: | Recurso digital |
| Langue: | anglais |
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2026
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| _version_ | 1866902290892324864 |
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| author | Perrin, Célia Courbot, Jean-Baptiste Leva, Yann Pierron, Romain |
| author_facet | Perrin, Célia Courbot, Jean-Baptiste Leva, Yann Pierron, Romain |
| contents | <p> </p> <p>This dataset is part of the <strong>Vineside</strong> project:</p> <ul> <li>The database is available on Zenodo.</li> <li>The corresponding preprint, describing the experimental conditions and results, is online on <a href="https://www.biorxiv.org/content/10.64898/2026.03.20.713180v1" target="_blank" rel="noopener">BioRxiv</a>.</li> <li>The code for reproducing the numerical experiments in the paper will be available on Github: <a title="https://github.com/courbot/vineside" href="https://github.com/courbot/vineside">https://github.com/courbot/vineside</a></li> </ul> <h3>Dataset description</h3> <p>This dataset comprises 4771 images of grapevine wood observed under microscope and macroscope.<br>The set of images is split into folders and sub-folders, following the experimental conditions. The subdivisions are highlighted in <strong>bold</strong> below. The main subdivision is the study:</p> <ul> <li><strong>I. Anatomy</strong> : wood was observed over 6 <strong>months</strong>.</li> <li><strong>II. Infection response</strong>: wood was observed when <strong>infected</strong>, and with a <strong>control</strong> and <strong>mock</strong> conditions.</li> </ul> <p>Two cultivars are studied: <strong>Gewurztraminer</strong> and <strong>Riesling</strong>.</p> <p>Each sample was observed along three directions:</p> <ul> <li><strong>Transversal</strong>: cross-section.</li> <li><strong>Radial</strong>: along a radius of the cane.</li> <li><strong>Tangential</strong>: longitudinal but parallel from the center axis.<br>These directions were observed in microscopy, with the complementary <strong>Transversal macroscope</strong>, to observe the full cross-section.</li> </ul> <p>Each experimental condition was observed over 10 to 15 <strong>samples</strong>, that is, 10 to 15 different plants.</p> <p>Microscope images were taken at <strong>x4</strong>, <strong>x10</strong>, and <strong>x40</strong> zoom levels.</p> <h3>Navigating the dataset</h3> <p>The dataset is organized as described above and may be explored by hand, without any specific tool.</p> <p>The map of the complete dataset is given in <code>file tree.txt</code>.</p> <p>To help gather images based on a selection of conditions, a Jupyter notebook in Python is also provided, under the name <code>Fetch.ipynb</code>.</p> <p>It requires standard Python packages, as well as Tifffile for reading .tif images (<a title="https://pypi.org/project/tifffile/" href="https://pypi.org/project/tifffile/">https://pypi.org/project/tifffile/</a>).<br>The package version under which the code was written is the following:</p> <ul> <li>Numpy: 2.3.4</li> <li>Tifffile: 2024.12.12</li> <li>Matplotlib: 3.10.6</li> <li>Pandas: 2.3.3</li> <li>Python: 3.12.12</li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18850060 |
| institution | Zenodo |
| language | eng |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Vineside - a microscopy dataset of grapevine wood anatomy over 6 months Perrin, Célia Courbot, Jean-Baptiste Leva, Yann Pierron, Romain Grapevine wood anatomy FasGa staining microscopy grapevine trunk diseases <p> </p> <p>This dataset is part of the <strong>Vineside</strong> project:</p> <ul> <li>The database is available on Zenodo.</li> <li>The corresponding preprint, describing the experimental conditions and results, is online on <a href="https://www.biorxiv.org/content/10.64898/2026.03.20.713180v1" target="_blank" rel="noopener">BioRxiv</a>.</li> <li>The code for reproducing the numerical experiments in the paper will be available on Github: <a title="https://github.com/courbot/vineside" href="https://github.com/courbot/vineside">https://github.com/courbot/vineside</a></li> </ul> <h3>Dataset description</h3> <p>This dataset comprises 4771 images of grapevine wood observed under microscope and macroscope.<br>The set of images is split into folders and sub-folders, following the experimental conditions. The subdivisions are highlighted in <strong>bold</strong> below. The main subdivision is the study:</p> <ul> <li><strong>I. Anatomy</strong> : wood was observed over 6 <strong>months</strong>.</li> <li><strong>II. Infection response</strong>: wood was observed when <strong>infected</strong>, and with a <strong>control</strong> and <strong>mock</strong> conditions.</li> </ul> <p>Two cultivars are studied: <strong>Gewurztraminer</strong> and <strong>Riesling</strong>.</p> <p>Each sample was observed along three directions:</p> <ul> <li><strong>Transversal</strong>: cross-section.</li> <li><strong>Radial</strong>: along a radius of the cane.</li> <li><strong>Tangential</strong>: longitudinal but parallel from the center axis.<br>These directions were observed in microscopy, with the complementary <strong>Transversal macroscope</strong>, to observe the full cross-section.</li> </ul> <p>Each experimental condition was observed over 10 to 15 <strong>samples</strong>, that is, 10 to 15 different plants.</p> <p>Microscope images were taken at <strong>x4</strong>, <strong>x10</strong>, and <strong>x40</strong> zoom levels.</p> <h3>Navigating the dataset</h3> <p>The dataset is organized as described above and may be explored by hand, without any specific tool.</p> <p>The map of the complete dataset is given in <code>file tree.txt</code>.</p> <p>To help gather images based on a selection of conditions, a Jupyter notebook in Python is also provided, under the name <code>Fetch.ipynb</code>.</p> <p>It requires standard Python packages, as well as Tifffile for reading .tif images (<a title="https://pypi.org/project/tifffile/" href="https://pypi.org/project/tifffile/">https://pypi.org/project/tifffile/</a>).<br>The package version under which the code was written is the following:</p> <ul> <li>Numpy: 2.3.4</li> <li>Tifffile: 2024.12.12</li> <li>Matplotlib: 3.10.6</li> <li>Pandas: 2.3.3</li> <li>Python: 3.12.12</li> </ul> |
| title | Vineside - a microscopy dataset of grapevine wood anatomy over 6 months |
| topic | Grapevine wood anatomy FasGa staining microscopy grapevine trunk diseases |
| url | https://doi.org/10.5281/zenodo.18850060 |