Vineside - a microscopy dataset of grapevine wood anatomy over 6 months

This dataset is part of the Vineside project: The database is available on Zenodo. The corresponding preprint, describing the experimental conditions and results, is online on BioRxiv. The code for reproducing the numerical experiments in the paper will be available on Github: https://github.com/courbot/vineside Dataset description This dataset comprises 4771 images of grapevine wood observed under microscope and macroscope.The set of images is split into folders and sub-folders, following the experimental conditions. The subdivisions are highlighted in bold below. The main subdivision is the study: I. Anatomy : wood was observed over 6 months. II. Infection response: wood was observed when infected, and with a control and mock conditions. Two cultivars are studied: Gewurztraminer and Riesling. Each sample was observed along three directions: Transversal: cross-section. Radial: along a radius of the cane. Tangential: longitudinal but parallel from the center axis.These directions were observed in microscopy, with the complementary Transversal macroscope, to observe the full cross-section. Each experimental condition was observed over 10 to 15 samples, that is, 10 to 15 different plants. Microscope images were taken at x4, x10, and x40 zoom levels. Navigating the dataset The dataset is organized as described above and may be explored by hand, without any specific tool. The map of the complete dataset is given in file tree.txt. To help gather images based on a selection of conditions, a Jupyter notebook in Python is also provided, under the name Fetch.ipynb. It requires standard Python packages, as well as Tifffile for reading .tif images (https://pypi.org/project/tifffile/).The package version under which the code was written is the following: Numpy: 2.3.4 Tifffile: 2024.12.12 Matplotlib: 3.10.6 Pandas: 2.3.3 Python: 3.12.12