erials and methods The protocol described in this peer-reviewed article is published on protocols.io, https://dx.doi.org/10.17504/protocols.io.bp2l6xo3zlqe/v1 , and is included for printing as S1 File with this article. Furthermore, three sets of high-resolution images yielded following the protocol are available from Zenodo at https://doi.org/10.5281/zenodo.10730414 . The high-resolution images were acquired between May and October 2023 in a Quercus serrata grove at the Kansai Research Center of the Forestry and Forest Products Research Institute (FFPRI) in Kyoto City, Japan (34°56’N, 135°46’E). The grove was located on a Cambisol [ 44 ] in flat terrain. Monthly mean air temperature ranged
Open resource ↗Zenodo · 10.5281/zenodo.10730414 · lines:31-38Unverified paper record
Assembly and application of a low-cost high-resolution imaging device for hyphae in soil.
PloS one · 24 Jan 2025 · 10.1371/journal.pone.0318083
Abstract
Soil imaging in the field and laboratory has greatly advanced our understanding of plant root systems. Soil fungi function as important plant symbionts and decomposers of complex organic material in soil environments. For fungal hyphae, however, the application of soil imaging remains scarce, limiting our understanding of hyphal systems in soil. This scarce application is partly due to the challenging development of a soil imaging device for hyphae: technical requirements to resolve fine hyphae (2-5 μm in diameter) are high, while the device cost must be low to facilitate sufficient deployment that can capture the high spatial heterogeneity of hyphal dynamics in soil. This protocol describes the do-it-yourself assembly and application of a low-cost high-resolution imaging device for observing hyphae in soil. The assembly of the open-source imaging device relies on many 3D-printed parts, reducing material costs to ca. 930 USD. The application of the imaging device yields soil profile images with a resolution of up to 0.52 μm px-1 (49000 dpi) within an observable volume of 70 × 210 × 1.5 mm. By repeatedly imaging a soil profile using the presented techniques, changes in the amount, distribution, and morphology of hyphae in soil can be observed and quantified.
Plant phenotyping relevance
土壌中の菌糸の量・分布・形態を画像から観察・定量する低コスト高解像度イメージング装置の組立・応用プロトコルであり、植物関連状態の取得手法が中心である。
abstractThis protocol describes the do-it-yourself assembly and application of a low-cost high-resolution imaging device for observing hyphae in soil.
abstractBy repeatedly imaging a soil profile using the presented techniques, changes in the amount, distribution, and morphology of hyphae in soil can be observed and quantified.
Code and data availability
The paper deposits its imaging-device design files, operating software, and high-resolution soil profile image sets on Zenodo, all paper-specific and publicly available.
l. The protocol is also available on protocols.io. (PDF) S1 Dataset Set of soil profile images acquired at focus depths of 0, 0.025, and 0.05 mm. Original images in the JPG format taken at an imaging resolution of 0.65 μm px -1 (39200 dpi). (ZIP) Data Availability Statement All design files used to assemble the imaging device ( https://doi.org/10.5281/zenodo.10689905 ), all software to operate the imaging device ( https://doi.org/10.5281/zenodo.10815832 ), and several sets of images yielded with the imaging device ( https://doi.org/10.5281/zenodo.10730414 ) are available from the data repository Zenodo. All remaining data are within the manuscript and its Supporting Information files.
Open resource ↗Zenodo · 10.5281/zenodo.10689905 · lines:147-155This is an automatically classified, unverified record. Curator approval is required before any resource enters the Catalog.