Data description

Purpose of data acquisition

The present dataset constitutes the first attempt at comparative micro-computed tomography (μCT) scanning of earthworm (Annelida: Clitellata: ‘Oligochaeta’) specimens. When used in combination with staining techniques that permit enhancing soft tissue contrast [1], μCT could become a promising technique for resolving pervasive issues in earthworm taxonomy and systematics. To this end, the application of μCT to freshly fixed and museum specimens was evaluated, and results were compared with data derived from traditional dissection techniques. The main methodological and taxonomical results of the study are presented in an accompanying publication [2].

The aim of the present report is to provide the earthworm research community with a reference dataset for future analyses of soft-bodied organisms based on non-destructive imaging techniques. In addition, uninhibited data access and enforced data deposition, as practiced here, are briefly discussed.

Scanned specimens

Scans of four lumbricid (‘Oligochaeta’: Lumbricidae) earthworm specimens are part of the present dataset. One freshly fixed and one museum specimen (stored in ethanol for several decades) were scanned for each of the two different species employed in the study, i.e. Aporrectodea caliginosa (Savigny, 1826) and Aporrectodea trapezoides (Dugès, 1828). All four specimens were stained using an ethanol-based phosphotungstic acid (PTA) solution, which was adapted from protocols described previously [3]. In order to increase the isotropic voxel resolution of the three-dimensional (3D) image stack, only the first ca. 35 segments of each specimen were scanned. These segments harbor all internal and external structures commonly used in earthworm taxonomy. Specific specimen data and supplementary image files have been deposited in the publicly accessible database of the Museum of Comparative Zoology, MCZbase (http://mczbase.mcz.harvard.edu/). In addition, hyperlinks to each specimen entry in MCZbase are provided on the dataset website in the GigaScience Database (GigaDB) online repository [4].

Data acquisition and processing

The four scans were produced using a μCT system equipped with a cone-beam tungsten X-ray source (SkyScan 1173, Bruker microCT, Kontich, Belgium). The specific scanning parameters are provided in the accompanying publication [2], and can also be found in the log file (.log) of each dataset folder available for download at GigaDB[4].

Each scan resulted in a set of 960 projection images in tagged image file format (TIFF, .tif). No binning protocols were employed during data acquisition. The projection images covered 2240 × 2240 pixels at 16-bit dynamic range. Reconstruction of the two-dimensional (2D) projection images into a 3D volumetric image stack was performed using the software NRecon 1.6.6.0 (Bruker microCT, Kontich, Belgium). This program runs under the reconstruction engine NReconServer 1.6.6, which employs a Feldkamp algorithm for volumetric reconstruction [5]. The two reconstruction parameters with significant effect on the quality of the final data were ring artifact and beam hardening correction. The output format for the 3D volumetric image stacks was bitmap image file (BMP, .bmp) at 8-bit dynamic range and 2240 × 2240 pixel size. In order to reduce final file size, the volume of interest (VOI) function, a 3D cropping tool, was used to remove all uninformative parts of the data following reconstruction. This resulted in changes to the pixel dimensions of each reconstructed image stack, but did not lead to spatial distortions in any of the three dimensions. Further information on the contents and size of both the projection and the reconstruction data folders is provided in Table 1.

Table 1 Overview of the earthworm dataset deposited in GigaDB
Full size table

Data quality

The quality of the data was ascertained through visual inspection of the scout projection and reconstruction images. Primary criteria were i) the full penetration of the sample by the staining agent and ii) the absence of artifacts. Although a total of eight scans were obtained in the course of the study, four of these scans were either trial scans or showed significant artifacts [2]. Therefore, only the four most representative scans have been deposited in GigaDB. Nonetheless, these scans represent the full taxonomic and morphological breadth of species and sample types included in the study. The imagery allows for an identification of numerous internal and external structures. No significant difference in the approach was observed when employing freshly fixed or museum specimens, nor between the two species analyzed.

Potential uses

The potential uses of the dataset presented here include morphometric or volumetric analyses of internal organs, studies of ingested sediment particles, the possibility of online collaborative dataset annotation, or interactive data exploration using digital 2D and 3D visualization tools.

The methodological approach itself is suitable for high-throughput scanning of hundreds or even thousands of earthworm specimens as well as other soft-bodied organisms [2]. This would result in large morphological taxon sampling, one of the prerequisites for broad taxonomic and systematic studies. Furthermore, non-invasive imaging techniques such as μCT leave specimens intact and generate digital data suitable for online dissemination, an important condition for effective data mining.

Availability and requirements

Data availability

The dataset is available at GigaDB and has a citable digital object identifier (DOI) [4]. Each of the eight folders has been packed using tape archiver (tar, .tar), before being compressed using GNU zip (gzip, .gz). The folders can be individually downloaded using a set of tools, e.g. File Transfer Protocol (FTP).

Dataset name: MicroCT scans of freshly fixed and museum earthworm specimens

Operating system: Platform-independent

License: Creative Commons 0 (CC0) public domain dedication (https://creativecommons.org/publicdomain/zero/1.0/)

Data requirements

Following download, the reconstructed images can, for example, be rapidly visualized using the ‘File:Import:Image Sequence’ command chain in the Java-based imaging software ImageJ (http://imagej.nih.gov/ij/). In addition, numerous other 2D and 3D visualization tools are available for free [6]. Given the size of the reconstructed image folders, a computer system with about 4 GB main random access memory (RAM) and 1 GB video RAM should be used.

Discussion

The dataset presented here permits full open access both to μCT-derived raw data (here: the projection images) as well as derivative data (here: the reconstructed image stacks). The availability of μCT raw data files has been deemed important, primarily due to the rapid increase in the performance of reconstruction algorithms, which in the future could lead to improved data reconstruction [7]. Furthermore, one reviewer as well as the editor of the accompanying publication [2] requested data deposition for purposes of data transparency, which was achieved here through storage and archiving of the dataset in GigaDB[4]. Despite these advances, a lack of coherent policy for data archiving and enforced data deposition in digital morphology remains [8], and metadata standards for data gathered using non-invasive imaging techniques are still not available [7].

Availability of supporting data

The dataset supporting the results of this article is available in the GigaScience Database online repository [4].