High-resolution images from a low-cost imaging device for hyphae in soil

This dataset contains high-resolution images produced by a low-cost imaging device for hyphae in soil called Hyphascope. Using a digital microscope camera (DMC; 600× magnification), the device takes detailed images (0.83 × 0.62 mm imaged area) of a soil profile from evenly spaced camera positions within a user-defined volume. Repeated imaging of a soil profile with Hyphascope enables researchers to observe and quantify changes in the amount, distribution, and morphology of hyphae.

Individual images were combined using the Grid/Collection stitching plugin of the Fiji distribution of imageJ (Preibisch et al. 2009). All images are supplied in the JPG format to limit their file size. For more details on the assembly and application of Hyphascope, see this protocol on protocols.io. For information on the development, limitations, and expected outcomes of the protocol, see this article published in PLOS ONE.  

Image set 1: 10 × 10 mm soil profile area at 20 - 30 mm soil depth

Imaged at 0.65 μm px-1 (39200 dpi)* in a Quercus serrata grove on 2023/05/25 during a period of high hyphal density in the soil.

Individual images (18 rows × 14 images each)

set1_foc00000.zip (focus depth 0 mm)

Combined images

set1_foc00000_combined.jpg (focus depth 0 mm)

Image set 2: 5 × 5 mm soil profile area at 100 - 105 mm soil depth

Imaged at 0.52 μm px-1 (49000 dpi) in a Quercus serrata grove on 2023/09/25.

Individual images (9 rows × 7 images each)

set1_foc00000.zip (focus depth 0 mm)

set1_foc00025zip (focus depth 0.025 mm)

set1_foc00050.zip (focus depth 0.05 mm)

Combined images

set1_foc00000_combined.jpg (focus depth 0 mm)

set1_foc00025_combined.jpg (focus depth 0.025 mm)

set1_foc00050_combined.jpg (focus depth 0.05 mm)

Image set 3: 5 × 5 mm soil profile area at soil surface level

Imaged at 0.52 μm px-1 (49000 dpi) in a Quercus serrata grove on 2023/10/14 during a rain event.

Individual images (9 rows × 7 images each)

set2_foc00000.zip (focus depth 0 mm)

set2_foc00025zip (focus depth 0.025 mm)

set2_foc00050.zip (focus depth 0.05 mm)

Combined images

set2_foc00000_combined.jpg (focus depth 0 mm)

set2_foc00025_combined.jpg (focus depth 0.025 mm)

set2_foc00050_combined.jpg (focus depth 0.05 mm)

*Units of imaging resolution:

pixel width (μm px-1), i.e. the horizontal or vertical distance on the imaged surface covered by a single pixel;

dots per inch (dpi), i.e. the number of pixels along a horizontal or vertical distance of 25.4 mm on the imaged surface.