DOI: 10.20350/digitalcsic/15672
title: MOSSAIC: MOSS Analysis Image Collection

description: [Material and methods] In this experiment six ground moss species were utilized. • Ptychostomum capillare (Hedw.) D.T. Holyoak & N. Pedersen [== Bryum capillare Hedw.] • Dicranum scoparium Hedw. • Homalothecium aureum H. Rob. • Hypnum cupressiforme Hedw. • Tortella squarrosa (Brid.) Limpr. [== Pleurochaete squarrosa (Brid.) Lindb.] • Syntrichia ruralis (Hedw.) F. Weber & D. Moh. For the moss stand inoculation, seedbed pots with synthetic wadding as the growth substrate were used. The experimental units were placed in three different locations along a 100-kilometer altitudinal gradient in Central Spain, specifically at: • Estación Biológica “El Ventorrillo” (VENT), Madrid, Spain (1482 meters above sea level - m.a.s.l.) • Universidad Autónoma de Madrid (UAM), Madrid, Spain (717 m.a.s.l.) • Finca Experimental “La Higueruela” (HIG), Toledo, Spain (455 m.a.s.l.) The pictures were captured using two Mapir Survey 2 cameras (https://www.mapir.camera/). One camera had an RGB sensor for visual wavelengths, while the other had a Red + NIR sensor for near-infrared. The manufacturer adjusted the focal distance to approximately 25 cm from the samples. Both cameras were equipped with a 16MP Sony Exmor IMX206 sensor, featuring a Bayer RGB pattern. The red absorption occurred at 660 nm, and near-infrared was captured at 850 nm. We employed a transparent plastic light diffuser box with an interior lining of white paper, such as filter paper. This setup served to even out the lighting and reduce the appearance of harsh shadows. Each image included the samples, a colour chart (specifically, the X-Rite ColorChecker® Classic) for calibration, as detailed in prior works (Ritchie et al., 2008; Fischer et al., 2012), and a millimetre scale for calculating the pixel-to-millimetre ratio. Moss samples were labelled in each hollow. The cameras saved the images in raw format and we converted it to tif format without compression using Darktable 2.6.1 software (https://www.darktable.org/) (‘Darktable’, 2019). Then we used ImageJ software (Schindelin et al., 2012) to align each pair of NIR-VIS images and to homogenize colour histograms for each VIS and NIR image series in each locality. The ImageJ scripts are provided by Photomoss protocol (Molina-Bustamante et al., 2022).
description: This dataset contains a set of images that display moss samples from six distinct species over seedling trays from a common garden experimental set-up. We grow these moss samples on a background of white synthetic material. The capture of the images was in both near-infrared and visible light wavelengths. We provide additional files to fit the main dataset objective: use it as a test platform for evaluating the PhotomossR package. In this repository, you will discover images taken in both the near-infrared and visible light spectrums. These images offer comprehensive data for testing different spectral indices using the PhotomossR package (Molina-Bustamante, DeCastro-Arrazola, Doherty, & Medina, 2022).
description: Contains 5 folders based on the locality and date of image capture. Within each locality folder, there are 4 subfolders (nir, vis, rois, mask) and a 'names.csv' file that provides label names for the samples. • "nir" folder with images in the infrared spectrum. Images named by the date of capture. • "vis" folder with images in the visible spectrum. Images named by the date of capture. • "rois" folder that includes roi files. Inside this folder, there are as many subfolders as images in “nir” and “vis” folders. Each subfolder containing the roi files corresponding to the samples we want to analyse in each of the images. • "mask" folder with binary images of moss samples. Files are numerically named.in the order PhotomossR will analyse it.