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 spirit stored specimens.  
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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==
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[[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==
 
==Introduction==
2D specimen imaging is a valuable addition to augment specimen records. 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.
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Specimen imaging is a way to augment specimen records. Quality digital images have a number of values including (but not limited to):  
==Value of digital imaging in spirit collections==
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* improved discovery of specimens  
Quality digital images have a number of values [[https://www.idigbio.org/wiki/images/7/7a/Sullivan-Value_of_Imaging-Ichthyology.pdf 1]] including (but not limited to):  
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* improved access to collection material  
# improved discovery of specimens  
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* potential research material  
# improved access to collection material  
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* dissemination to the public
# potential research material  
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# dissemination to the public
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== Workflows and guides==
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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.
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.
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== Equipment ==
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==2D Imaging==
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].  
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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.
==Immersion tanks==
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===Equipment===
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]].  
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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].
=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.  
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=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]].
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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===
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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===
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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:
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* iDigBio Wiki - Digitization Resources https://www.idigbio.org/wiki/index.php/Digitization_Resources
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* iDigBio Documentation - Digitization https://www.idigbio.org/documentation/digitization
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Information about imaging herbarium specimens:
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* 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/
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* New York Botanic Gardens: Digitization Resources - https://sweetgum.nybg.org/science/information-management/digitization/digitization-resources/
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* JSTOR Global Plants type specimen imaging: Partner Resources - https://guides.jstor.org/plants-partners
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==3D Imaging==
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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==
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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.
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* [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.]
  
==Contributors==
 
Andrew D. Williston
 
 
==Source Material==
 
==Source Material==
  
 
== Links ==
 
== Links ==
1. [https://www.idigbio.org/wiki/images/7/7a/Sullivan-Value_of_Imaging-Ichthyology.pdf Sullivan, J. P.  2016. The Value of Imaging Specimens in Ichthyology. iDigBio Vertebrate Digitization Workshop, Berkeley, CA, April 4 - 6, 2016]<br />
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* [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)]
2. https://www.idigbio.org/wiki/index.php/Developing_Robust_Object_to_Image_to_Data_(DROID3)<br />
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* [https://www.idigbio.org/content/workflow-modules-and-task-lists| iDigBio Digitization Workflow Modules and Task Lists]
3. www.idigbio.org/content/workflow-modules-and-task-lists<br />
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4. http://silurus.ansp.org/ACSI/corresp/digital_imaging_tips.html<br />
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5. https://vimeo.com/61663146<br />
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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.<br />
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7.iDigBio 2014. iDigBio Imaging Equipment Recommendations https://www.idigbio.org/wiki/images<br />/8/86/IDigBioImagingGeneralEquipmentRecommendations1_0.pdf<br />
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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<br />
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9. http://mcz.harvard.edu/Departments/Ichthyology/fish_imaging.html<br />
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=== Consensus Documents ===
 
=== Consensus Documents ===
  
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<references/>
 
<references/>
  
[[Category:Desired BP Content]] [[Category:Imaging]]
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[[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

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:

Information about imaging herbarium specimens:

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

Consensus Documents

Community Standards

Review Documents

References