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. 2015 Sep 21;2:150052. doi: 10.1038/sdata.2015.52

High-resolution computed tomography reconstructions of invertebrate burrow systems

Rachel Hale 1,a, Richard Boardman 2, Mark N Mavrogordato 2, Ian Sinclair 2, Trevor J Tolhurst 3, Martin Solan 1
PMCID: PMC4576671  PMID: 26396743

Abstract

The architecture of biogenic structures can be highly influential in determining species contributions to major soil and sediment processes, but detailed 3-D characterisations are rare and descriptors of form and complexity are lacking. Here we provide replicate high-resolution micro-focus computed tomography (μ-CT) data for the complete burrow systems of three co-occurring, but functionally contrasting, sediment-dwelling inter-tidal invertebrates assembled alone, and in combination, in representative model aquaria. These data (≤2,000 raw image slices aquarium−1, isotropic voxel resolution, 81 μm) provide reference models that can be used for the development of novel structural analysis routines that will be of value within the fields of ecology, pedology, geomorphology, palaeobiology, ichnology and mechanical engineering. We also envisage opportunity for those investigating transport networks, vascular systems, plant rooting systems, neuron connectivity patterns, or those developing image analysis or statistics related to pattern or shape recognition. The dataset will allow investigators to develop or test novel methodology and ideas without the need to generate a complete three-dimensional computation of exemplar architecture.

Subject terms: Animal behaviour, Ecosystem ecology, 3-D reconstruction, Biooceanography

Background & Summary

Soils and sediments provide habitat for a wide range of organisms and the vertical exploitation of this ecospace has been important in mediating major ecosystem properties and the diversification of life over geological timescales1–3. Insights about organism-sediment relations, however, have largely been restricted to two dimensions4,5, although important inferences about burrowing mechanics6 and three dimensional architecture7 have been made from burrow castings8 and the use of optically transparent sediment analogues9. Relatively few studies apply non-invasive interrogation of intact sedimentary media10–13, despite significant advances in optical and clinical imaging technology14. High-resolution micro-focus computed tomography (μ-CT) offers a way of not only imaging the organisms themselves15,16 but also visualising the structure of a whole sediment core in three dimensions to allow quantitative examination of organismal burrowing17.

Experimental details are given in Hale et al.18. Briefly, surficial sediment (less than 3 cm depth; mean particle size, 54.80 μm; mud content, 55.93%) and three co-occurring functionally contrasting inter-tidal invertebrates (the polychaete Hediste diversicolor, the gastropod Hydrobia ulvae and mud shrimp Corophium volutator) were collected from the mid-shore at Breydon water, Great Yarmouth, UK (N52° 37.030′, E01° 41.390′) and returned to the Biodiversity and Ecosystem Futures Facility at the University of Southampton to acclimatise to laboratory conditions (5 days). Sediment was sieved (500 μm mesh) in a seawater (sand filtered, UV sterilized and salinity 33 practical salinity units) bath to remove macrofauna and allowed to settle for 48 h to retain the fine fraction (less than 63 μm). Circular aquaria (internal diameter=10 cm, 15 cm tall, n=20) were filled to a depth of 8 cm with sediment homogenate overlain by 4 cm of seawater.

Overlying seawater was replaced after 24 h to remove excess nutrients associated with assembly. Aquaria were aerated and maintained at 12±0.1 °C under a 12:12 h light (Aqualine T5 Reef White 10 K fluorescent light tubes, Aqua Medic) cycle. Fauna were not added until the lower regions of the sediment cores showed evidence of reducing conditions (visible anoxic microniche formation). Replicate (n=5) invertebrate communities (1 g wet weight aquaria−1; ~127 g m−2) were assembled in monoculture (Hediste diversicolor, HD; Hydrobia ulvae, HU; or Corophium volutator, CV) and in equal mixture (Mix).

These μ-CT sediment scans can provide reference models which may be of use in a range of connected fields, such as for the development of novel structural analysis routines and computer models in ecology17,19, pedology20, geomorphology, ichnology21, palaeobiology, and mechanical engineering22. We envisage those investigating transport networks23, vascular systems, plant rooting systems24, neuron connectivity patterns25,26, or developing image analysis or statistics related to pattern or shape recognition will find these data of interest. We have made this dataset available to allow investigators to develop or test novel methodology and ideas without the need to generate a complete three-dimensional computation of exemplar architecture.

Methods

Reconstruction of biogenic structures in the aquaria was achieved using a 225/450 kVp Nikon/Metris custom designed micro-focus computed tomography scanner housed within the μ-VIS X-ray Imaging Centre, University of Southampton. As the system used to acquire the scan data requires the cores to be held vertically batches of 5 aquaria were stacked and secured in a custom-made holding brace to ensure stability and prevent sediment or seawater leakage during rotation and scanning (Fig. 1). During each acquisition, the aquaria were rotated through 360° whilst collecting 3,142 projections averaging over 8 frames per 250 ms projection (for a total of 2 s per projection, ca. 105 min per acquisition). Ring artifact reduction was enabled. X-ray conditions were set to 300 kVp and 326 μA with a 3 mm Cu filter, and an XRD 1621 CN3 H5 PerkinElmer flat panel detector (CsI scintillator) was used to collect the images. In the resulting reconstructed images, levels of grey scale reflect the level of X-ray attenuation caused by variation in bulk density3. Hence, brighter pixels represent denser material (sediment) and darker pixels represent less dense material (burrow voids). Raw image slices (n=2,000 aquarium−1, voxel resolution=81 μm) were processed as follows: First, the projection data was reconstructed using CTPro3D (v. XT 2.2 service pack 10, Nikon Metrology, UK) and CTAgent (v. XT 2.2 service pack 10, Nikon Metrology, UK). The reconstructed volumes were converted to 8 bit format using FIJI27 (Version 1.49a) to reduce file sizes and computational loading. Finally, these images were opened as a 3D project in VGStudio Max (v. 2.1 Volume Graphics GmbH, Germany) and an edge-preserving 3D 5 pixel non-linear digital median filter was applied to reduce noise in the images.

Figure 1. Five aquaria stacked in the holding brace in the micro-focus computed tomography scanner housed within the μ-VIS X-ray Imaging Centre, University of Southampton.

Figure 1

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Three types of images were produced. Whole core scans of 16-bit quality (Core_Volume_01_16bit to Core_Volume_20_16bit: Data Citation 1), processed image whole core scans of 8-bit quality with a 3D 5 pixel non-linear digital median filter applied (Core_Volume_01 to Core_Volume_20: Data Citation 1), an example slice of which is shown in Fig. 2, and processed burrow images (Burrow_Volume_01 to Burrow_Volume_20: Data Citation 1). To produce the burrow images the three-dimensional image captured of the aquaria and the holding brace was discarded to leave the central sediment core volume. Within the sediment core, regions of interest, the low density burrows, were segmented using a threshold based seed point growing algorithm that identified three-dimensional areas of similar low densities to produce a three-dimensional image of the burrow network (Fig. 3) called the burrow volume.

Figure 2. A representative transverse core slice from the Core Volumes image set showing distinct low density burrows (dark grey) through the (light grey) higher density sediment.

Figure 2

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A Core Volume image set consists of number images that are sequentially stacked to create the three-dimensional core volume image. The central sediment core is 10 cm in diameter.

Figure 3. Representative example reconstructed three-dimensional burrow models for (a) Hediste diversicolor, (b) Hydrobia ulvae, (c) Corophium volutator, and (d) the three species in mixture created from the stacked Burrow Volumes images in VG Studio.

Figure 3

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The sediment cores containing the burrows are 10 cm in diameter.

Data Records

All data records listed in this section are available at the Harvard Dataverse (Data Citation 1). Details of supplementary experimental procedures and additional materials, including videos of the three dimensional burrow structures are available from Hale et al.18. Computed tomography three-dimensional files have been converted to stacked tagged image file format (TIFF) images with associated dimension data (image width, image breadth, stack height) to enable access by multiple processing programs. There are three sets of images (n=20). Sediment core volume images for each replicate in 16- bit (Core_Volume_01_16bit to Core_Volume_20_16bit) and 8- bit (Core_Volume_01 to Core_Volume_20) and burrow volume images for each replicate (Burrow_Volume_01 to Burrow_Volume_20).

Technical Validation

The system geometry at the μ-VIS X-ray Imaging Centre, University of Southampton, is checked and validated periodically using a 3 ruby sphere reference object that has been measured using optical profilometry (Xyris 4000 CL Surface Profiler, Taicaan technologies Europe). The centroid distances (threshold independent) of these ruby spheres when measured using CT are in agreement with the optical profilometry measurements to within 0.2%. For the presented scans, measurement validation was carried out post-scan by ensuring reference distances were accurately represented in the final images (within 1%).

Usage Notes

The TIFF images provided should be imported as a three dimensional image sequence. The starting image is 0. The number of images and dimensions of each stack for each sediment core or burrow volume is provided in Tables 1,2,3 (available online only). When importing, image names should be sorted numerically.

Table 1. Stacked image data for the 16-bit quality unfiltered sediment core volumes (n=20).

Core_ID Scan_ID Replicate_ID Species_ID dimension_X dimension_y dimension_Z number_of_images species_id_folder stack_folder imagestack_fileprefix first_image last_image
34 1 Rep_01 Corophium volutator 2000 2000 2000 2000 Species_Corophium Core_Volume_01_CV01_16bit Core_Volume_01_CV01_16bit_2000_2000_2000_ Core_Volume_01_CV01_16bit_2000_2000_2000_0000.tif Core_Volume_01_CV01_16bit_2000_2000_2000_1999.tif
24 2 Rep_01 Hediste diversicolor 2000 2000 2000 2000 Species_Hediste Core_Volume_02_HD01_16bit Core_Volume_02_HD01_16bit_2000_2000_2000_ Core_Volume_02_HD01_16bit_2000_2000_2000_0000.tif Core_Volume_02_HD01_16bit_2000_2000_2000_1999.tif
39 3 Rep_01 Mixed species 2000 2000 2000 2000 Species_Mixed Core_Volume_03_Mx01_16bit Core_Volume_03_Mx01_16bit_2000_2000_2000_ Core_Volume_03_Mx01_16bit_2000_2000_2000_0000.tif Core_Volume_03_Mx01_16bit_2000_2000_2000_1999.tif
29 4 Rep_01 Hydrobia ulvae 2000 2000 2000 2000 Species_Hydrobia Core_Volume_04_HU01_16bit Core_Volume_04_HU01_16bit_2000_2000_2000_ Core_Volume_04_HU01_16bit_2000_2000_2000_0000.tif Core_Volume_04_HU01_16bit_2000_2000_2000_1999.tif
40 5 Rep_02 Mixed species 2000 2000 2000 2000 Species_Mixed Core_Volume_05_Mx02_16bit Core_Volume_05_Mx02_16bit_2000_2000_2000_ Core_Volume_05_Mx02_16bit_2000_2000_2000_0000.tif Core_Volume_05_Mx02_16bit_2000_2000_2000_1999.tif
23 6 Rep_02 Hediste diversicolor 2000 2000 2000 2000 Species_Hediste Core_Volume_06_HD02_16bit Core_Volume_06_HD02_16bit_2000_2000_2000_ Core_Volume_06_HD02_16bit_2000_2000_2000_0000.tif Core_Volume_06_HD02_16bit_2000_2000_2000_1999.tif
36 7 Rep_03 Mixed species 2000 2000 2000 2000 Species_Mixed Core_Volume_07_Mx03_16bit Core_Volume_07_Mx03_16bit_2000_2000_2000_ Core_Volume_07_Mx03_16bit_2000_2000_2000_0000.tif Core_Volume_07_Mx03_16bit_2000_2000_2000_1999.tif
31 8 Rep_02 Corophium volutator 2000 2000 2000 2000 Species_Corophium Core_Volume_08_CV02_16bit Core_Volume_08_CV02_16bit_2000_2000_2000_ Core_Volume_08_CV02_16bit_2000_2000_2000_0000.tif Core_Volume_08_CV02_16bit_2000_2000_2000_1999.tif
30 9 Rep_02 Hydrobia ulvae 2000 2000 2000 2000 Species_Hydrobia Core_Volume_09_HU02_16bit Core_Volume_09_HU02_16bit_2000_2000_2000_ Core_Volume_09_HU02_16bit_2000_2000_2000_0000.tif Core_Volume_09_HU02_16bit_2000_2000_2000_1999.tif
25 10 Rep_03 Hediste diversicolor 2000 2000 2000 2000 Species_Hediste Core_Volume_10_HD03_16bit Core_Volume_10_HD03_16bit_2000_2000_2000_ Core_Volume_10_HD03_16bit_2000_2000_2000_0000.tif Core_Volume_10_HD03_16bit_2000_2000_2000_1999.tif
28 11 Rep_03 Hydrobia ulvae 2000 2000 2000 2000 Species_Hydrobia Core_Volume_11_HU03_16bit Core_Volume_11_HU03_16bit_2000_2000_2000_ Core_Volume_11_HU03_16bit_2000_2000_2000_0000.tif Core_Volume_11_HU03_16bit_2000_2000_2000_1999.tif
38 12 Rep_04 Mixed species 2000 2000 2000 2000 Species_Mixed Core_Volume_12_Mx04_16bit Core_Volume_12_Mx04_16bit_2000_2000_2000_ Core_Volume_12_Mx04_16bit_2000_2000_2000_0000.tif Core_Volume_12_Mx04_16bit_2000_2000_2000_1999.tif
22 13 Rep_04 Hediste diversicolor 2000 2000 2000 2000 Species_Hediste Core_Volume_13_HD04_16bit Core_Volume_13_HD04_16bit_2000_2000_2000_ Core_Volume_13_HD04_16bit_2000_2000_2000_0000.tif Core_Volume_13_HD04_16bit_2000_2000_2000_1999.tif
27 14 Rep_04 Hydrobia ulvae 2000 2000 2000 2000 Species_Hydrobia Core_Volume_14_HU04_16bit Core_Volume_14_HU04_16bit_2000_2000_2000_ Core_Volume_14_HU04_16bit_2000_2000_2000_0000.tif Core_Volume_14_HU04_16bit_2000_2000_2000_1999.tif
35 15 Rep_03 Corophium volutator 2000 2000 2000 2000 Species_Corophium Core_Volume_15_CV03_16bit Core_Volume_15_CV03_16bit_2000_2000_2000_ Core_Volume_15_CV03_16bit_2000_2000_2000_0000.tif Core_Volume_15_CV03_16bit_2000_2000_2000_1999.tif
32 16 Rep_04 Corophium volutator 2000 2000 2000 2000 Species_Corophium Core_Volume_16_CV04_16bit Core_Volume_16_CV04_16bit_2000_2000_2000_ Core_Volume_16_CV04_16bit_2000_2000_2000_0000.tif Core_Volume_16_CV04_16bit_2000_2000_2000_1999.tif
37 17 Rep_05 Mixed species 2000 2000 2000 2000 Species_Mixed Core_Volume_17_Mx05_16bit Core_Volume_17_Mx05_16bit_2000_2000_2000_ Core_Volume_17_Mx05_16bit_2000_2000_2000_0000.tif Core_Volume_17_Mx05_16bit_2000_2000_2000_1999.tif
33 18 Rep_05 Corophium volutator 2000 2000 2000 2000 Species_Corophium Core_Volume_18_CV05_16bit Core_Volume_18_CV05_16bit_2000_2000_2000_ Core_Volume_18_CV05_16bit_2000_2000_2000_0000.tif Core_Volume_18_CV05_16bit_2000_2000_2000_1999.tif
26 19 Rep_05 Hydrobia ulvae 2000 2000 2000 2000 Species_Hydrobia Core_Volume_19_HU05_16bit Core_Volume_19_HU05_16bit_2000_2000_2000_ Core_Volume_19_HU05_16bit_2000_2000_2000_0000.tif Core_Volume_19_HU05_16bit_2000_2000_2000_1999.tif
21 20 Rep_05 Hediste diversicolor 2000 2000 2000 2000 Species_Hediste Core_Volume_20_HD05_16bit Core_Volume_20_HD05_16bit_2000_2000_2000_ Core_Volume_20_HD05_16bit_2000_2000_2000_0000.tif Core_Volume_20_HD05_16bit_2000_2000_2000_1999.tif
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Table 2. Stacked image data for the 8-bit quality sediment core volumes with 3D 5 pixel non-linear digital median filtered applied (n=20).

Core_ID Scan_ID Replicate_ID Species_ID dimension_X dimension_y dimension_Z number_of_images species_id_folder stack_folder imagestack_fileprefix first_image last_image
34 1 Rep_01 Corophium volutator 1230 1230 700 700 Species_Corophium Core_Volume_01_CV01 Core_Volume_01_CV01_1230_1230_700_ Core_Volume_01_CV01_1230_1230_700_0000.tif Core_Volume_01_CV01_1230_1230_700_0699.tif
24 2 Rep_01 Hediste diversicolor 1701 1401 928 928 Species_Hediste Core_Volume_02_HD01 Core_Volume_02_HD01_1701_1401_928_ Core_Volume_02_HD01_1701_1401_928_0000.tif Core_Volume_02_HD01_1701_1401_928_0927.tif
39 3 Rep_01 Mixed species 1401 1401 892 892 Species_Mixed Core_Volume_03_Mx01 Core_Volume_03_Mx01_1401_1401_892_ Core_Volume_03_Mx01_1401_1401_892_0000.tif Core_Volume_03_Mx01_1401_1401_829_0828.tif
29 4 Rep_01 Hydrobia ulvae 1501 1501 1201 1201 Species_Hydrobia Core_Volume_04_HU01 Core_Volume_04_HU01_1501_1501_1201_ Core_Volume_04_HU01_1501_1501_1201_0000.tif Core_Volume_04_HU01_1501_1501_1201_1200.tif
40 5 Rep_02 Mixed species 1207 1217 923 923 Species_Mixed Core_Volume_05_Mx02 Core_Volume_05_Mx02_1207_1217_923_ Core_Volume_05_Mx02_1207_1217_923_0000.tif Core_Volume_05_Mx02_1207_1217_923_0922.tif
23 6 Rep_02 Hediste diversicolor 1601 1601 1401 1401 Species_Hediste Core_Volume_06_HD02 Core_Volume_06_HD02_1601_1601_1401_ Core_Volume_06_HD02_1601_1601_1401_0000.tif Core_Volume_06_HD02_1601_1601_1401_1400.tif
36 7 Rep_03 Mixed species 1501 1501 1101 1101 Species_Mixed Core_Volume_07_Mx03 Core_Volume_07_Mx03_1501_1501_1101_ Core_Volume_07_Mx03_1501_1501_1101_0000.tif Core_Volume_07_Mx03_1501_1501_1101_1100.tif
31 8 Rep_02 Corophium volutator 1501 1501 1401 1401 Species_Corophium Core_Volume_08_CV02 Core_Volume_08_CV02_1501_1501_1401_ Core_Volume_08_CV02_1501_1501_1401_0000.tif Core_Volume_08_CV02_1501_1501_1401_1400.tif
30 9 Rep_02 Hydrobia ulvae 1501 1501 801 801 Species_Hydrobia Core_Volume_09_HU02 Core_Volume_09_HU02_1501_1501_801_ Core_Volume_09_HU02_1501_1501_801_0000.tif Core_Volume_09_HU02_1501_1501_801_0800.tif
25 10 Rep_03 Hediste diversicolor 2000 2000 2000 2000 Species_Hediste Core_Volume_10_HD03 Core_Volume_10_HD03_2000_2000_2000_ Core_Volume_10_HD03_2000_2000_2000_0000.tif Core_Volume_10_HD03_2000_2000_2000_1999.tif
28 11 Rep_03 Hydrobia ulvae 1501 1501 1001 1001 Species_Hydrobia Core_Volume_11_HU03 Core_Volume_11_HU03_1501_1501_1001_ Core_Volume_11_HU03_1501_1501_1001_0000.tif Core_Volume_11_HU03_1501_1501_1001_1000.tif
38 12 Rep_04 Mixed species 1601 1601 1301 1301 Species_Mixed Core_Volume_12_Mx04 Core_Volume_12_Mx04_1601_1601_1301_ Core_Volume_12_Mx04_1601_1601_1301_0000.tif Core_Volume_12_Mx04_1601_1601_1301_1300.tif
22 13 Rep_04 Hediste diversicolor 1601 1601 1301 1301 Species_Hediste Core_Volume_13_HD04 Core_Volume_13_HD04_1601_1601_1301_ Core_Volume_13_HD04_1601_1601_1301_0000.tif Core_Volume_13_HD04_1601_1601_1301_1300.tif
27 14 Rep_04 Hydrobia ulvae 1601 1601 951 951 Species_Hydrobia Core_Volume_14_HU04 Core_Volume_14_HU04_1601_1601_951_ Core_Volume_14_HU04_1601_1601_951_0000.tif Core_Volume_14_HU04_1601_1601_951_0950.tif
35 15 Rep_03 Corophium volutator 1601 1601 1201 1201 Species_Corophium Core_Volume_15_CV03 Core_Volume_15_CV03_1601_1601_1201_ Core_Volume_15_CV03_1601_1601_1201_0000.tif Core_Volume_15_CV03_1601_1601_1201_1200.tif
32 16 Rep_04 Corophium volutator 1601 1601 1001 1001 Species_Corophium Core_Volume_16_CV04 Core_Volume_16_CV04_1601_1601_1001_ Core_Volume_16_CV04_1601_1601_1001_0000.tif Core_Volume_16_CV04_1601_1601_1001_1000.tif
37 17 Rep_05 Mixed species 1601 1601 1501 1501 Species_Mixed Core_Volume_17_Mx05 Core_Volume_17_Mx05_1601_1601_1501_ Core_Volume_17_Mx05_1601_1601_1501_0000.tif Core_Volume_17_Mx05_1601_1601_1501_1500.tif
33 18 Rep_05 Corophium volutator 1601 1601 1201 1201 Species_Corophium Core_Volume_18_CV05 Core_Volume_18_CV05_1601_1601_1201_ Core_Volume_18_CV05_1601_1601_1201_0000.tif Core_Volume_18_CV05_1601_1601_1201_1200.tif
26 19 Rep_05 Hydrobia ulvae 1601 1601 1101 1101 Species_Hydrobia Core_Volume_19_HU05 Core_Volume_19_HU05_1601_1601_1101_ Core_Volume_19_HU05_1601_1601_1101_0000.tif Core_Volume_19_HU05_1601_1601_1101_1100.tif
21 20 Rep_05 Hediste diversicolor 1601 1601 1401 1401 Species_Hediste Core_Volume_20_HD05 Core_Volume_20_HD05_1601_1601_1401_ Core_Volume_20_HD05_1601_1601_1401_0000.tif Core_Volume_20_HD05_1601_1601_1401_1400.tif
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Table 3. Stacked image data for the burrow volumes (n=20).

Core_ID Scan_ID Replicate_ID Species_ID dimension_X dimension_y dimension_Z number_of_images species_id_folder stack_folder imagestack_fileprefix first_image last_image
34 1 Rep_01 Corophium volutator 1229 1184 265 265 Species_Corophium Burrow_Volume_01_CV01 Burrow_Volume_01_CV01_1229_1184_265_ Burrow_Volume_01_CV01_1229_1184_265_000.tif Burrow_Volume_01_CV01_1229_1184_265_264.tif
24 2 Rep_01 Hediste diversicolor 1207 1219 909 909 Species_Hediste Burrow_Volume_02_HD01 Burrow_Volume_02_HD01_1207_1219_909_ Burrow_Volume_02_HD01_1207_1219_909_000.tif Burrow_Volume_02_HD01_1207_1219_909_908.tif
39 3 Rep_01 Mixed species 1219 1236 872 872 Species_Mixed Burrow_Volume_03_Mx01 Burrow_Volume_03_Mx01_1219_1236_872_ Burrow_Volume_03_Mx01_1219_1236_872_000.tif Burrow_Volume_03_Mx01_1219_1236_872_871.tif
29 4 Rep_01 Hydrobia ulvae 1220 1133 411 411 Species_Hydrobia Burrow_Volume_04_HU01 Burrow_Volume_04_HU01_1220_1133_411_ Burrow_Volume_04_HU01_1220_1133_411_000.tif Burrow_Volume_04_HU01_1220_1133_411_410.tif
40 5 Rep_02 Mixed species 1205 1215 900 900 Species_Mixed Burrow_Volume_05_Mx02 Burrow_Volume_05_Mx02_1205_1215_900_ Burrow_Volume_05_Mx02_1205_1215_900_000.tif Burrow_Volume_05_Mx02_1205_1215_900_899.tif
23 6 Rep_02 Hediste diversicolor 1228 1224 906 906 Species_Hediste Burrow_Volume_06_HD02 Burrow_Volume_06_HD02_1228_1224_906_ Burrow_Volume_06_HD02_1228_1224_906_000.tif Burrow_Volume_06_HD02_1228_1224_906_905.tif
36 7 Rep_03 Mixed species 1228 1223 898 898 Species_Mixed Burrow_Volume_07_Mx03 Burrow_Volume_07_Mx03_1228_1223_898_ Burrow_Volume_07_Mx03_1228_1223_898_000.tif Burrow_Volume_07_Mx03_1228_1223_898_897.tif
31 8 Rep_02 Corophium volutator 1123 1121 220 220 Species_Corophium Burrow_Volume_08_CV02 Burrow_Volume_08_CV02_1123_1121_220_ Burrow_Volume_08_CV02_1123_1121_220_000.tif Burrow_Volume_08_CV02_1123_1121_220_219.tif
30 9 Rep_02 Hydrobia ulvae 900 1212 313 313 Species_Hydrobia Burrow_Volume_09_HU02 Burrow_Volume_09_HU02_900_1212_313_ Burrow_Volume_09_HU02_900_1212_313_000.tif Burrow_Volume_09_HU02_900_1212_313_312.tif
25 10 Rep_03 Hediste diversicolor 1220 1235 854 854 Species_Hediste Burrow_Volume_10_HD03 Burrow_Volume_10_HD03_1220_1235_854_ Burrow_Volume_10_HD03_1220_1235_854_000.tif Burrow_Volume_10_HD03_1220_1235_854_853.tif
28 11 Rep_03 Hydrobia ulvae 1129 1188 332 332 Species_Hydrobia Burrow_Volume_11_HU03 Burrow_Volume_11_HU03_1129_1188_332_ Burrow_Volume_11_HU03_1129_1188_332_000.tif Burrow_Volume_11_HU03_1129_1188_332_331.tif
38 12 Rep_04 Mixed species 1228 1223 879 879 Species_Mixed Burrow_Volume_12_Mx04 Burrow_Volume_12_Mx04_1228_1223_879_ Burrow_Volume_12_Mx04_1228_1223_879_000.tif Burrow_Volume_12_Mx04_1228_1223_879_878.tif
22 13 Rep_04 Hediste diversicolor 1236 1222 943 943 Species_Hediste Burrow_Volume_13_HD04 Burrow_Volume_13_HD04_1236_1222_943_ Burrow_Volume_13_HD04_1236_1222_943_000.tif Burrow_Volume_13_HD04_1236_1222_943_942.tif
27 14 Rep_04 Hydrobia ulvae 1204 1151 305 305 Species_Hydrobia Burrow_Volume_14_HU04 Burrow_Volume_14_HU04_1204_1151_305_ Burrow_Volume_14_HU04_1204_1151_305_000.tif Burrow_Volume_14_HU04_1204_1151_305_304.tif
35 15 Rep_03 Corophium volutator 1204 1191 252 252 Species_Corophium Burrow_Volume_15_CV03 Burrow_Volume_15_CV03_1204_1191_252_ Burrow_Volume_15_CV03_1204_1191_252_000.tif Burrow_Volume_15_CV03_1204_1191_252_251.tif
32 16 Rep_04 Corophium volutator 1201 1168 274 274 Species_Corophium Burrow_Volume_16_CV04 Burrow_Volume_16_CV04_1201_1168_274_ Burrow_Volume_16_CV04_1201_1168_274_000.tif Burrow_Volume_16_CV04_1201_1168_274_273.tif
37 17 Rep_05 Mixed species 1228 1244 981 981 Species_Mixed Burrow_Volume_17_Mx05 Burrow_Volume_17_Mx05_1228_1244_981_ Burrow_Volume_17_Mx05_1228_1244_981_000.tif Burrow_Volume_17_Mx05_1228_1244_981_980.tif
33 18 Rep_05 Corophium volutator 1179 1195 332 332 Species_Corophium Burrow_Volume_18_CV05 Burrow_Volume_18_CV05_1179_1195_332_ Burrow_Volume_18_CV05_1179_1195_332_000.tif Burrow_Volume_18_CV05_1179_1195_332_331.tif
26 19 Rep_05 Hydrobia ulvae 1207 1140 335 335 Species_Hydrobia Burrow_Volume_19_HU05 Burrow_Volume_19_HU05_1207_1140_335_ Burrow_Volume_19_HU05_1207_1140_335_000.tif Burrow_Volume_19_HU05_1207_1140_335_334.tif
21 20 Rep_05 Hediste diversicolor 1235 1218 859 859 Species_Hediste Burrow_Volume_20_HD05 Burrow_Volume_20_HD05_1235_1218_859_ Burrow_Volume_20_HD05_1235_1218_859_000.tif Burrow_Volume_20_HD05_1235_1218_859_858.tif
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There are no limitations on data use.

Additional Information

Tables 1,2,3 are only available in the online version of this paper.

How to cite this article: Hale, R. et al. High-resolution computed tomography reconstructions of invertebrate burrow systems. Sci. Data 2:150052 doi: 10.1038/sdata.2015.52 (2015).

Supplementary Material

sdata201552-isa1.zip (3KB, zip)

Acknowledgments

This work was undertaken while R.H. was in receipt of a University of East Anglia Funded PhD studentship. R.H. thanks the University of East Anglia for additional financial support for travel and subsistence while in Southampton. Financial support for μ-CT was provided by the University of Southampton. We thank Dr Louise Darroch at the British Oceanographic Data Centre for her assistance with metadata organisation. We thank the Harvard Dataverse for hosting our data and Sonia Barbosa, Kevin Condon and Dwayne Liburd for their technical assistance. This work was partially supported by NERC grant NE/K001906/1.

Footnotes

The authors declare no competing financial interests.

Data Citations

  1. Hale R., Boardman R., Mavrogordato M. N., Sinclair I., Tolhurst T. J., Solan M. 2015. Harvard Dataverse. http://dx.doi.org/10.7910/DVN/4XNRE3 [DOI] [PMC free article] [PubMed]

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Citations

  1. Hale R., Boardman R., Mavrogordato M. N., Sinclair I., Tolhurst T. J., Solan M. 2015. Harvard Dataverse. http://dx.doi.org/10.7910/DVN/4XNRE3 [DOI] [PMC free article] [PubMed]

Supplementary Materials

sdata201552-isa1.zip (3KB, zip)

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