Work Description

University of Michigan Museum of Zoology Computed Tomography Datasets

The University of Michigan Museum of Zoology (UMMZ) is the center for the study of animal diversity on campus, focusing on the evolutionary origins of the planet’s animal species, the genetic information they contain and the communities and ecosystems they help form. Now an integral part of the Department of Ecology and Evolutionary Biology (EEB), the UMMZ houses world-class collections, containing more than 15 million specimens, spanning almost 200 years of regional and global biodiversity studies, and that support a multi-faceted Departmental research and teaching program.

This file provides a generalized description of each computed tomography (CT) dataset deposited on Deep Blue Data, as well as some instructions for usage of these data. Each data deposit represents a physical voucher specimen archived in the UMMZ permanent research collections. As such, the usage of each dataset is subject to the terms and conditions of the UMMZ. For current guidelines, please visit the UMMZ website (https://lsa.umich.edu/ummz).

Methodology

This dataset was created at the University of Michigan Museum of Zoology (UMMZ) using a procedure involving computed tomography (CT) hardware. After retrieving the specimen from the museum's collection, staff secured the specimen in the Nikon XT H 225 ST and initiated the scanning process, which included capturing projections by rotating the specimen. The device's associated software CT-Pro-3D and the projections were then used to reconstruct a set of TIFF images, with each corresponding to a slice of the three-dimensional object (one voxel in height). In addition, the software created an .xtek volume file (included here), which contains details about the scanning environment, projections, and reconstructions.

“DiceCT” refers to “diffusible iodine contrast enhanced computed tomography”. DiceCT scans are conducted to visualize the soft tissue anatomy of the scanned specimen. To do this each specimen is stained in 1.25% Lugol’s iodine (1L = 25 g KI + 12.5 I2 + 1L deionized H20) for 1-8 weeks, size dependent. Prior to staining each specimen is stepped down from 70% ETOH to 50% ETOH to 25% ETOH. Following scanning the specimen is then stepped up back to 70% ETOH to destain and remove the Lugol’s iodine from the specimen.

Naming Convention

All datasets produced by the University of Michigan Museum of Zoology (UMMZ) Micro(µ)CT Scanning Laboratory are labeled in accordance with the “Darwin Core” naming convention for natural history collections. Please see https://www.tdwg.org/standards/dwc/ for more information.

As such, each dataset name will appear as an alphanumeric string consisting of five to six segments:

1. The institution where the voucher specimen originated (i.e., ummz).
2. The collection in which the voucher specimen is archived (e.g., birds, fish, insects, herps, mammals, or mollusks).
3. The catalog number of the voucher specimen
4. The generic name of the voucher specimen as listed in the collections database
5. The specific epithet of the voucher specimen as listed in the collections database.
6. A modifier indicating the region of interest scanned, or type of scan in the case of a diceCT scan. If it is a full body-skeletal scan then there will not be a modifier in the sixth segment.

An example of a dataset name (numbers indicate parts described above):

UMMZ-Herps-57533_Osteocephalus-pearsoni_skull
(1) (2) (3) (4) (5) (6)

Folder and File Descriptions

“Raw” Zipped Datasets - These datasets are denoted by a “Raw-” prefix followed by the scanned ROI (whole body/skull/diceCT/etc). These datasets contain the unprocessed tiff radiograph images produced by the Nikon XT H 225 ST Micro(µ)CT scanner. These files are not useful for 3D rendering in a segmentation program. They are useful for re-reconstructing a dataset at a later date if needed.

“Recon” Zipped Datasets - These datasets are denoted by a “Recon-” prefix followed by the scanned ROI (whole body/skull/diceCT/etc). These datasets contain the processed tiff tomogram images produced by the proprietary reconstruction software. These files are used for 3D rendering in a segmentation program.

XTEKCT file - This text file can be found in both the zipped “Raw” and “Recon” folders. This file contains critical information related to the parameters of the scan. When opened, a user may use this file to find the voxel size (X/Y/Z) for the scan, reported in millimeters (mm). The voxel resolution will be required to import the reconstructed tiff tomograms into a segmentation program.

VGL file - This is an automatically generated Volume Graphics project file found in the zipped “Recon” folder. If you are using Volume Graphics to render your 3D dataset, then you may use this file to begin your project. If you do not have access to Volume Graphics, then this file can be ignored.

[vg-project] folder - This folder can be found in the zipped “Recon” folder and contains metadata. The files in this folder are used to generate a volume graphics project and do not need to be accessed by the user, but are needed for background processes.

_CentreSlice folder - This folder can be found in the zipped “Raw” folder and contains metadata. This folder contains metadata related to the CT scan acquisition and does not need to be accessed regularly by the user.

_ctdata file - This text file is found in the zipped “Raw” folder and contains projection information for each image taken. This folder contains metadata related to the CT scan acquisition and does not need to be accessed by the user.

CT Information file - This html file (.ctinfo) is found in the zipped “Raw” folder. This file contains metadata related to the name of the dataset, and does not need to be accessed by the user.

CT Profile file - This html file (.ctinfo) is found in the zipped “Raw” folder.. This file contains metadata related to the scanning parameters of the dataset, and does not need to be accessed regularly by the user.

Useful Programs for 3D Visualization

* 3D Slicer [free] - https://www.slicer.org/
* Avizo - https://www.thermofisher.com/us/en/home/industrial/electron-microscopy/electron-microscopy-instruments-workflow-solutions/3d-visualization-analysis-software.html
* Dragonfly [free] - https://www.theobjects.com/dragonfly/index.html
* Mimics - https://www.materialise.com/en/medical/mimics-innovation-suite/mimics
* Volume Graphics - https://www.volumegraphics.com/