Difference between revisions of "3D Imaging"
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== Statement of Purpose == | == Statement of Purpose == | ||
| − | 3D, or three-dimensional, imaging as a digitization process for collections | + | Understanding of (and standards for) 3D, or three-dimensional, imaging as a digitization process for natural history collections. |
==Introduction== | ==Introduction== | ||
| − | + | "3D imaging" refers to a wide range of techniques for the visualization and characterization of specimens in three dimensions. These techniques can be separated into two groups: those which result in aligned stacks (or "volumes") of 2D images, and those which result in a surface models. Volumes contain information throughout the interior of a specimen, while surface models usually characterize only the outer shape and possibly appearance of a specimen. Surface models can be calculated from volumes, or created directly, but volumes can not be made from surface models. Concerns specific to museum applications of the most common 3D imaging techniques are explored in greater detail under Modalities, below. | |
==Contributors== | ==Contributors== | ||
| + | [[user:Jon Woodward|Jon Woodward]] | ||
| + | ==Modalities== | ||
| + | The most common techniques for museum collections are listed here. For further info, see [https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/895/2137 Brecko & Mathys, 2020], [https://www.researchgate.net/publication/332762580_Micro-computed_tomography_for_natural_history_specimens_a_handbook_of_best_practice_protocols Keklikoglou et. al., 2019]. | ||
| − | === | + | ===Micro-CT=== |
| + | Micro-CT uses a series of x-ray images of a specimen, captured at incrementing rotation, to calculate density values throughout the specimen. This calculation is usually referred to as "reconstruction." These density values are represented as black & white pixels in a stack of 2D images. These reconstructed images are the output of the process, and can be used in a variety of downstream applications. Micro-CT requires specialized (and quite expensive) equipment and software, and both the scan and the reconstruction can be time-consuming. Each CT scan generates a significant amount of data, as both the x-ray source images and reconstruction images can easily number in the thousands. See the [[Microtomography (microCT)]] page for more info. | ||
| − | === | + | ===MRI=== |
| + | |||
| + | ===Structure from Motion=== | ||
| + | Also known as "SfM," and often referred to in shorthand as "photogrammetry," Structure from Motion uses images of the exterior of a specimen (or the interior of a space), captured at many different rotational angles relative to the specimen. Software then calculates the surface topology of the specimen. Per Brecko & Mathys, "The technique itself is quite fast, inexpensive and open to anyone with a camera and the basic knowledge of how to use it." The process results in a surface model, with or without an image texture. | ||
| + | |||
| + | ===Laser Scanning=== | ||
| + | |||
| + | ===Structured Light Scanning=== | ||
| + | |||
| + | ===3D Reconstruction from Stacked 2D Images=== | ||
| + | 2D images of physical sections of a specimen can be aligned and stacked, resulting in a 3D volume. Such images are often created during (or after) a process that consumes the specimen, such as images of scanned serial histological sections, or images of the grinding face of a serially ground paleontological specimen. Without reference points, images can be difficult to align, so prior knowledge of the specimen is essential. See [https://pubmed.ncbi.nlm.nih.gov/29502034/ Pichat et. al., 2018]. | ||
| + | |||
| + | ==Archiving== | ||
| + | As with any digital imaging process, archival principles are important for 3D image data. These include capturing and saving metadata along with the image file(s), and storing the file(s) in a lossless format where possible. The [https://www.idigbio.org/wiki/index.php/OVert:_Open_Exploration_of_Vertebrate_Diversity_in_3D#Protocols_&_Workflows Overt TCN's] protocol and data standards are available on the TCN wiki. [https://wiki.duke.edu/display/MD/MorphoSource+Documentation+Home Morphosource], a popular repository for 3D data, enforces data and metadata quality standards. | ||
| + | |||
| + | ==Distribution and Downstream Use== | ||
==Source Material== | ==Source Material== | ||
Latest revision as of 19:51, 29 May 2023
Contents
Statement of Purpose
Understanding of (and standards for) 3D, or three-dimensional, imaging as a digitization process for natural history collections.
Introduction
"3D imaging" refers to a wide range of techniques for the visualization and characterization of specimens in three dimensions. These techniques can be separated into two groups: those which result in aligned stacks (or "volumes") of 2D images, and those which result in a surface models. Volumes contain information throughout the interior of a specimen, while surface models usually characterize only the outer shape and possibly appearance of a specimen. Surface models can be calculated from volumes, or created directly, but volumes can not be made from surface models. Concerns specific to museum applications of the most common 3D imaging techniques are explored in greater detail under Modalities, below.
Contributors
Modalities
The most common techniques for museum collections are listed here. For further info, see Brecko & Mathys, 2020, Keklikoglou et. al., 2019.
Micro-CT
Micro-CT uses a series of x-ray images of a specimen, captured at incrementing rotation, to calculate density values throughout the specimen. This calculation is usually referred to as "reconstruction." These density values are represented as black & white pixels in a stack of 2D images. These reconstructed images are the output of the process, and can be used in a variety of downstream applications. Micro-CT requires specialized (and quite expensive) equipment and software, and both the scan and the reconstruction can be time-consuming. Each CT scan generates a significant amount of data, as both the x-ray source images and reconstruction images can easily number in the thousands. See the Microtomography (microCT) page for more info.
MRI
Structure from Motion
Also known as "SfM," and often referred to in shorthand as "photogrammetry," Structure from Motion uses images of the exterior of a specimen (or the interior of a space), captured at many different rotational angles relative to the specimen. Software then calculates the surface topology of the specimen. Per Brecko & Mathys, "The technique itself is quite fast, inexpensive and open to anyone with a camera and the basic knowledge of how to use it." The process results in a surface model, with or without an image texture.
Laser Scanning
Structured Light Scanning
3D Reconstruction from Stacked 2D Images
2D images of physical sections of a specimen can be aligned and stacked, resulting in a 3D volume. Such images are often created during (or after) a process that consumes the specimen, such as images of scanned serial histological sections, or images of the grinding face of a serially ground paleontological specimen. Without reference points, images can be difficult to align, so prior knowledge of the specimen is essential. See Pichat et. al., 2018.
Archiving
As with any digital imaging process, archival principles are important for 3D image data. These include capturing and saving metadata along with the image file(s), and storing the file(s) in a lossless format where possible. The Overt TCN's protocol and data standards are available on the TCN wiki. Morphosource, a popular repository for 3D data, enforces data and metadata quality standards.
