Difference between revisions of "Digital Imaging"
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==Introduction== | ==Introduction== | ||
| − | Specimen imaging is a way to augment specimen records. Quality digital images have a number of values | + | 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== | ==2D Imaging== | ||
| − | == Equipment == | + | Two-dimensional imaging, or 2D imaging, is what the majority of images generated are. This is often achieved with a camera, but can also be done with a CAT scan or MRI. |
| + | ===Equipment=== | ||
There is an wide range of photographic equipment available. Gear, particularly camera bodies, change rapidly. iDigBio has assembled a guide with equipment reccomendations[https://www.idigbio.org/wiki/images/8/86/IDigBioImagingGeneralEquipmentRecommendations1_0.pdf 7]. | There is an wide range of photographic equipment available. Gear, particularly camera bodies, change rapidly. iDigBio has assembled a guide with equipment reccomendations[https://www.idigbio.org/wiki/images/8/86/IDigBioImagingGeneralEquipmentRecommendations1_0.pdf 7]. | ||
| + | ===File Formats=== | ||
| − | ===Liquid Collections 2D Imaging=== | + | ====Liquid Collections 2D 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. | 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. | ||
| − | ==== Workflows and | + | =====Workflows and Guides===== |
Explicit workflows are helpful, particularly for new imaging technicians who might not understand best practices working with spirit stored collections and/or little experience with imaging. Workflows are intended to help all technicians work with quality, efficiency, and with best practices for specimen handling. [[iDigBio DROID3 working group (Developing_Robust Object to Image to Data)[[https://www.idigbio.org/wiki/index.php/Developing_Robust_Object_to_Image_to_Data_(DROID3) 2]] has developed detailed workflows that can be used to help start or improve an existing wet specimen digital imaging project. Initial task list modules have been developed by this group [[http://www.idigbio.org/content/workflow-modules-and-task-lists 3]] and are currently being revised. Additional guides to image capture and editing of fish specimens are available [[http://silurus.ansp.org/ACSI/corresp/digital_imaging_tips.html 4]],[[https://vimeo.com/61663146 5]],[[https://www.idigbio.org/wiki/images/d/d1/SabajPerez_2009_textonly.pdf 6]] It should be noted that equipment suggestions change rapidly. | Explicit workflows are helpful, particularly for new imaging technicians who might not understand best practices working with spirit stored collections and/or little experience with imaging. Workflows are intended to help all technicians work with quality, efficiency, and with best practices for specimen handling. [[iDigBio DROID3 working group (Developing_Robust Object to Image to Data)[[https://www.idigbio.org/wiki/index.php/Developing_Robust_Object_to_Image_to_Data_(DROID3) 2]] has developed detailed workflows that can be used to help start or improve an existing wet specimen digital imaging project. Initial task list modules have been developed by this group [[http://www.idigbio.org/content/workflow-modules-and-task-lists 3]] and are currently being revised. Additional guides to image capture and editing of fish specimens are available [[http://silurus.ansp.org/ACSI/corresp/digital_imaging_tips.html 4]],[[https://vimeo.com/61663146 5]],[[https://www.idigbio.org/wiki/images/d/d1/SabajPerez_2009_textonly.pdf 6]] It should be noted that equipment suggestions change rapidly. | ||
| − | ====Immersion tanks==== | + | =====Immersion tanks===== |
Wet specimens are best photographed when immersed in fluid. This serves a dual purpose preventing specimen drying as well as reducing glare on the specimen’s surface that might obscure surface detail. Both horizontal and vertical immersion tanks are used to hold wet specimens for imaging[[https://www.idigbio.org/wiki/images/0/00/IDigBio-Berkeley_USE.pdf 8]]. | Wet specimens are best photographed when immersed in fluid. This serves a dual purpose preventing specimen drying as well as reducing glare on the specimen’s surface that might obscure surface detail. Both horizontal and vertical immersion tanks are used to hold wet specimens for imaging[[https://www.idigbio.org/wiki/images/0/00/IDigBio-Berkeley_USE.pdf 8]]. | ||
* Vertical tank - Vertical tanks resemble typical aquarium tanks but are generally narrow and tall. A plate of glass within the tank is used to gently press and sandwich the specimen against the front glass pane of the aquarium. Vertical tanks require camera mount in front of the tank, such as a tripod. Benefits of vertical tanks are cleaner backgrounds, setup mobility, and lighting flexibility. They are well suited for both in-collection and field use. | * Vertical tank - Vertical tanks resemble typical aquarium tanks but are generally narrow and tall. A plate of glass within the tank is used to gently press and sandwich the specimen against the front glass pane of the aquarium. Vertical tanks require camera mount in front of the tank, such as a tripod. Benefits of vertical tanks are cleaner backgrounds, setup mobility, and lighting flexibility. They are well suited for both in-collection and field use. | ||
* Horizontal tank - Horizontal tanks can be useful for specimens that need extensive and delicate manipulations and posing, like uncurling or pinning. Sheet glass is sometimes place on curled fish specimens to hold them posed. Horizontal tanks are usually used in combination with a copy stand. An example can be found on the MCZ Ichthyology website[[http://mcz.harvard.edu/Departments/Ichthyology/fish_imaging.html 9]]. | * Horizontal tank - Horizontal tanks can be useful for specimens that need extensive and delicate manipulations and posing, like uncurling or pinning. Sheet glass is sometimes place on curled fish specimens to hold them posed. Horizontal tanks are usually used in combination with a copy stand. An example can be found on the MCZ Ichthyology website[[http://mcz.harvard.edu/Departments/Ichthyology/fish_imaging.html 9]]. | ||
| + | ==3D Imaging== | ||
| + | Three-dimensional imaging is a less common and more expensive form of imaging and is often achieved by SEM, TEM, and laser scans. | ||
| + | |||
| + | ===Equipment=== | ||
| + | ===File Formats=== | ||
| + | |||
| + | ==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. | ||
| + | * Sullivan, John P., ''The Value of Imaging Specimens in Ichthyology'', 2016. [[https://www.idigbio.org/wiki/images/7/7a/Sullivan-Value_of_Imaging-Ichthyology.pdf 1]] | ||
==Source Material== | ==Source Material== | ||
Revision as of 17:35, 10 November 2022
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 - Liquid collection imaging;
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, but can also be done with a CAT scan or MRI.
Equipment
There is an wide range of photographic equipment available. Gear, particularly camera bodies, change rapidly. iDigBio has assembled a guide with equipment reccomendations7.
File Formats
Liquid Collections 2D 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.
Workflows and Guides
Explicit workflows are helpful, particularly for new imaging technicians who might not understand best practices working with spirit stored collections and/or little experience with imaging. Workflows are intended to help all technicians work with quality, efficiency, and with best practices for specimen handling. [[iDigBio DROID3 working group (Developing_Robust Object to Image to Data)[2] has developed detailed workflows that can be used to help start or improve an existing wet specimen digital imaging project. Initial task list modules have been developed by this group [3] and are currently being revised. Additional guides to image capture and editing of fish specimens are available [4],[5],[6] It should be noted that equipment suggestions change rapidly.
Immersion tanks
Wet specimens are best photographed when immersed in fluid. This serves a dual purpose preventing specimen drying as well as reducing glare on the specimen’s surface that might obscure surface detail. Both horizontal and vertical immersion tanks are used to hold wet specimens for imaging[8].
- Vertical tank - Vertical tanks resemble typical aquarium tanks but are generally narrow and tall. A plate of glass within the tank is used to gently press and sandwich the specimen against the front glass pane of the aquarium. Vertical tanks require camera mount in front of the tank, such as a tripod. Benefits of vertical tanks are cleaner backgrounds, setup mobility, and lighting flexibility. They are well suited for both in-collection and field use.
- Horizontal tank - Horizontal tanks can be useful for specimens that need extensive and delicate manipulations and posing, like uncurling or pinning. Sheet glass is sometimes place on curled fish specimens to hold them posed. Horizontal tanks are usually used in combination with a copy stand. An example can be found on the MCZ Ichthyology website[9].
3D Imaging
Three-dimensional imaging is a less common and more expensive form of imaging and is often achieved by SEM, TEM, and laser scans.
Equipment
File Formats
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.
- Sullivan, John P., The Value of Imaging Specimens in Ichthyology, 2016. [1]
Source Material
Links
1. Sullivan, J. P. 2016. The Value of Imaging Specimens in Ichthyology. iDigBio Vertebrate Digitization Workshop, Berkeley, CA, April 4 - 6, 2016
2. https://www.idigbio.org/wiki/index.php/Developing_Robust_Object_to_Image_to_Data_(DROID3)
3. www.idigbio.org/content/workflow-modules-and-task-lists
4. http://silurus.ansp.org/ACSI/corresp/digital_imaging_tips.html
5. https://vimeo.com/61663146
6. Sabaj Pérez, Mark H. "Photographic atlas of fishes of the Guiana Shield." Bulletin of the Biological Society of Washington 17.1 (2009): 52-59.
7.iDigBio 2014. iDigBio Imaging Equipment Recommendations https://www.idigbio.org/wiki/images
/8/86/IDigBioImagingGeneralEquipmentRecommendations1_0.pdf
8. Randall, Z. 2016. Imaging Systems: Light Box vs. Copy Stand vs. Squeeze Tank https://www.idigbio.org/wiki/images/0/00/IDigBio-Berkeley_USE.pdf
9. http://mcz.harvard.edu/Departments/Ichthyology/fish_imaging.html
