Difference between revisions of "Digital Imaging"
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== About == | == About == | ||
| − | These links and documents contain information about best practices for digital imaging of | + | These links and documents contain information about best practices for digital imaging of specimens. Both 2D and 3D imaging can be very important to collections and achieved in a variety of ways. This page will house workflows and links to external resources on protocols and recommendations for imaging specimens of all kinds in 2D and 3D. |
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==Contributors== | ==Contributors== | ||
| − | Andrew D. Williston | + | [[user:AndrewWilliston|Andrew D. Williston]]; [[user:GenevieveTocci| Genevieve E. Tocci]]; [[user:Shelley James| Shelley A. James]]; [[user:Alana Rivera| Alana Rivera]] |
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| + | ==Introduction== | ||
| + | Specimen imaging is a way to augment specimen records. Quality digital images have a number of values including (but not limited to): | ||
| + | * improved discovery of specimens | ||
| + | * improved access to collection material | ||
| + | * potential research material | ||
| + | * dissemination to the public | ||
| + | |||
| + | Before undertaking a large amount of imaging there are several practical considerations to address. Firstly, digital image files can be very large and will need to be stored in a way that is safe and retrievable long term. There can be issues with file formats changing over time as well as storage mediums. No storage is free, and even if the image size is small, a large number of small images can need a large amount of storage. Secondly, a consistent naming format and way to link images back with the physical collections. If there is no way to go back to see what specimen an image belongs to it can be very problematic for research and use. | ||
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| + | ==2D Imaging== | ||
| + | Two-dimensional imaging, or 2D imaging, is what the majority of images generated are. This is often achieved with a camera or x-ray. This includes techniques like focus stacking. | ||
| + | ===Equipment=== | ||
| + | There is an wide range of photographic equipment and imaging software programs available. Both hardware and software changes rapidly and can be very object dependent. [https://www.idigbio.org/sites/default/files/workshop-presentations/small-herbarium2013/iDigBioImagingEquipmentRecommendations1_0.pdf| iDigBio has assembled a guide with equipment recommendations]. | ||
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| + | The SPNHC Wiki hopes to have recommendations and links based on the imaging project type (fluid vs. dry, large depth of field vs. shallow, etc.). Please check on the relevant pages linked to and watch for additional content. | ||
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| + | ===Fluid Collections Imaging=== | ||
| + | Spirit specimens face some unique imaging challenges because of their wet storage. Use and further development of these best practices is intended to improve quality and efficiency of spirit collection digital imaging. Details on imaging fluid collections are found on the [[Fluid_Collection_Imaging| Fluid Collection Imaging]] wiki page. | ||
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| + | ===Dry Specimen Imaging=== | ||
| + | The SPNHC Wiki plans to have generate additional pages related to this content, including information on focus stacking, imaging flat specimens, and other workflows based on specimen type and previous large digitization project standards. Please check on the relevant pages linked to and watch for additional content. Additionally please see the pages at iDigBio: | ||
| + | * iDigBio Wiki - Digitization Resources https://www.idigbio.org/wiki/index.php/Digitization_Resources | ||
| + | * iDigBio Documentation - Digitization https://www.idigbio.org/documentation/digitization | ||
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| + | Information about imaging herbarium specimens: | ||
| + | * Managers of Australasian Herbarium Collections (MAHC - Australia): Guidelines for Imaging Type Specimens of Algae, Bryophytes, Fungi and Lichens - https://chah.gov.au/documents-and-guidelines/ | ||
| + | * New York Botanic Gardens: Digitization Resources - https://sweetgum.nybg.org/science/information-management/digitization/digitization-resources/ | ||
| + | * JSTOR Global Plants type specimen imaging: Partner Resources - https://guides.jstor.org/plants-partners | ||
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| + | ==3D Imaging== | ||
| + | Three-dimensional imaging is a less common and more expensive form of imaging. It is often achieved by CT and MRI, which produced 2D images that are stacked at a volume and can be manipulated in 3D. Additional techniques are SEM, TEM, and laser scans. | ||
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| + | Details on 3D imaging collections are found on the [[3D_Imaging| 3D Imaging]] wiki page. | ||
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| + | ==Advocacy for Imaging== | ||
| + | Images of specimens, and the process of imaging is something that has clear value to those work in collections. The process is also expensive and labor intensive, which can often require advocacy to achieve. Here are a list of references and resources related to the value of imaging collections. | ||
| + | * [https://www.idigbio.org/wiki/images/7/7a/Sullivan-Value_of_Imaging-Ichthyology.pdf Sullivan, John P., ''The Value of Imaging Specimens in Ichthyology'', 2016.] | ||
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==Source Material== | ==Source Material== | ||
== Links == | == Links == | ||
| − | + | * [https://www.idigbio.org/wiki/index.php/Developing_Robust_Object_to_Image_to_Data_(DROID3)| iDigBio wiki - Developing Robust Object to Image to Data (DROID3)] | |
| − | + | * [https://www.idigbio.org/content/workflow-modules-and-task-lists| iDigBio Digitization Workflow Modules and Task Lists] | |
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=== Consensus Documents === | === Consensus Documents === | ||
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<references/> | <references/> | ||
| − | [[Category:Desired BP Content]] [[Category:Imaging]] | + | [[Category:Desired BP Content]][[Category:Digitization and Imaging]][[Category:Zoology Collections]][[Category:Botanical Collections]][[Category:Geology and Paleontology Collections]][[Category:Collection Management]] |
Latest revision as of 17:50, 29 May 2023
Contents
About
These links and documents contain information about best practices for digital imaging of specimens. Both 2D and 3D imaging can be very important to collections and achieved in a variety of ways. This page will house workflows and links to external resources on protocols and recommendations for imaging specimens of all kinds in 2D and 3D.
Contributors
Andrew D. Williston; Genevieve E. Tocci; Shelley A. James; Alana Rivera
Introduction
Specimen imaging is a way to augment specimen records. Quality digital images have a number of values including (but not limited to):
- improved discovery of specimens
- improved access to collection material
- potential research material
- dissemination to the public
Before undertaking a large amount of imaging there are several practical considerations to address. Firstly, digital image files can be very large and will need to be stored in a way that is safe and retrievable long term. There can be issues with file formats changing over time as well as storage mediums. No storage is free, and even if the image size is small, a large number of small images can need a large amount of storage. Secondly, a consistent naming format and way to link images back with the physical collections. If there is no way to go back to see what specimen an image belongs to it can be very problematic for research and use.
2D Imaging
Two-dimensional imaging, or 2D imaging, is what the majority of images generated are. This is often achieved with a camera or x-ray. This includes techniques like focus stacking.
Equipment
There is an wide range of photographic equipment and imaging software programs available. Both hardware and software changes rapidly and can be very object dependent. iDigBio has assembled a guide with equipment recommendations.
The SPNHC Wiki hopes to have recommendations and links based on the imaging project type (fluid vs. dry, large depth of field vs. shallow, etc.). Please check on the relevant pages linked to and watch for additional content.
Fluid Collections Imaging
Spirit specimens face some unique imaging challenges because of their wet storage. Use and further development of these best practices is intended to improve quality and efficiency of spirit collection digital imaging. Details on imaging fluid collections are found on the Fluid Collection Imaging wiki page.
Dry Specimen Imaging
The SPNHC Wiki plans to have generate additional pages related to this content, including information on focus stacking, imaging flat specimens, and other workflows based on specimen type and previous large digitization project standards. Please check on the relevant pages linked to and watch for additional content. Additionally please see the pages at iDigBio:
- iDigBio Wiki - Digitization Resources https://www.idigbio.org/wiki/index.php/Digitization_Resources
- iDigBio Documentation - Digitization https://www.idigbio.org/documentation/digitization
Information about imaging herbarium specimens:
- Managers of Australasian Herbarium Collections (MAHC - Australia): Guidelines for Imaging Type Specimens of Algae, Bryophytes, Fungi and Lichens - https://chah.gov.au/documents-and-guidelines/
- New York Botanic Gardens: Digitization Resources - https://sweetgum.nybg.org/science/information-management/digitization/digitization-resources/
- JSTOR Global Plants type specimen imaging: Partner Resources - https://guides.jstor.org/plants-partners
3D Imaging
Three-dimensional imaging is a less common and more expensive form of imaging. It is often achieved by CT and MRI, which produced 2D images that are stacked at a volume and can be manipulated in 3D. Additional techniques are SEM, TEM, and laser scans.
Details on 3D imaging collections are found on the 3D Imaging wiki page.
Advocacy for Imaging
Images of specimens, and the process of imaging is something that has clear value to those work in collections. The process is also expensive and labor intensive, which can often require advocacy to achieve. Here are a list of references and resources related to the value of imaging collections.
Source Material
Links
- iDigBio wiki - Developing Robust Object to Image to Data (DROID3)
- iDigBio Digitization Workflow Modules and Task Lists
