DOC

Summary of discussions - SERNEC - Appalachian State University

By Maurice Hunter,2014-10-20 22:20
15 views 0
Summary of discussions - SERNEC - Appalachian State Universityof,State,state

    Summary of discussions by the Live Plant Imaging subgroup of the Imaging Standards working group of SERNEC

    Compiled by Steve Baskauf, Vanderbilt University Dept. of Biological Sciences

Background

    Recommendations Related to the Collection of Live Plant Images and Creation of a SERNEC Live Plant Image Collection (April 2008) http://www.sernec.org/files/recommendations.pdf

    Baskauf, S.J. and B.K. Kirchoff (2008) Digital plant images as specimens: toward standards for photographing living plants. Vulpina 7:16-30

    http://www.cals.ncsu.edu/plantbiology/ncsc/vulpia/pdf/Baskauf_&_Kirchoff_Digital_Plant_Images.pdf

Goals and Logistics

    The major goal of this group is to work toward the establishment of a SERNEC Live Plant Image Collection. In order to accomplish this goal, the Live Plant Imaging subgroup is discussing issues that need to be resolved to lay the groundwork for the establishment of the collection. The participants

    - with experience taking a significant number of live plant images

    - with an interest in or responsibility for maintaining a collection of live plant images - with an interest in using live plant images to create educational products After discussion we hope to reach a consensus on the issues that would allow creation of the collection to go forward.

Participants

    The following individuals participated in the discussion to varying degrees.

Steve Baskauf

    Bioimages plant image website; Vanderbilt University

    steve.baskauf@vanderbilt.edu

    http://bioimages.vanderbilt.edu

Paul Davison

    bryophyte images; University of North Alabama

    pgdavison@una.edu

    http://www2.una.edu/pdavis/SchusterPlants.htm

Jonathan Evans

    Director, Sewanee Herbarium; University of the South

    jevans@sewanee.edu

    http://lal.sewanee.edu/herbarium/index.htm

Darel Hess

    plant photographer

    darelhess@netscape.net

Timothy M. Jones

    Carex taxonomy, interactive keys; Louisiana State University

    tjone54@lsu.edu

Bruce K. Kirchoff

    visual, computer-based plant learning; UNC Greensboro

    kirchoff@uncg.edu

http://www.mbgpress.info/index.php?task=id&id=08025

Joseph LaForest

    Center for Invasive Species and Ecosystem Health (Bugwood Network), University of Georgia

    laforest@uga.edu

    http://www.forestryimages.org/

Victor Ma

    collections manager; University of Tennessee herbarium qma@utk.edu

    http://tenn.bio.utk.edu/vascular/vascular.html

Zack Murrell

    SERNEC Director; Appalachian State University murrellze@appstate.edu

    http://www.sernec.org/

Robert H Neidlinger

    plant photographer; assistant curator Western Kentucky University herbarium

    robert.neidlinger@wku.edu

Debra Paul

    Morphbank

    dpaul@scs.fsu.edu

    http://www.morphbank.net/

Jeffrey S. Pippen

    plant images; Nicholas School of the Environment and Earth Sciences, Duke University

    jspippen@duke.edu

    http://www.duke.edu/~jspippen/plants/plants.htm

Derick Poindexter

    SERNEC Project Manager; Appalachian State University poindexterdb@appstate.edu

    http://www.sernec.org/

Daniel W. Reed

    plant photographer; Wildflowers of the Southeastern United States website

    daniel@2bnthewild.com

    http://2bnthewild.com/index2.shtml

Steve Seiberling

    digital imaging specialist, University of North Carolina Herbarium

    sseiber@email.unc.edu

    http://www.herbarium.unc.edu/

Alan Weakley

    Curator, University of North Carolina Herbarium; Flora of the Southeast

    weakley@unc.edu

    http://www.herbarium.unc.edu/

B. Eugene Wofford

    Director, University of Tennessee Herbarium bewofford@utk.edu

    http://tenn.bio.utk.edu/vascular/vascular.html

    Major topics of discussion (outlined May 16, 2008)

The following major topics of discussion were identified with discussion to proceed sequentially

    through the topics.

    1. Licensing issues (e.g. what flavor of Creative Commons license would we adopt as the most

    restrictive allowable license that a participant could apply to contributed images, an understanding about what would be "fair game" for use of images in the collection without a permission request, how would the participating institution or individual be recognized and

    associated with images in the collection)

    2. Imaging standards (e.g. what standards should be adopted as guidelines for the way images are taken and the type of metadata collected along with the images, how should "legacy images"

    (high quality and reliably identified images that don't meet some of these standards) be

    incorporated into the collection?)

    3. Best practices for image collection (e.g. the logistics of collecting images, archiving them,

    and assembling the database that would allow users to find the images they need).

    Summary of first round of discussion (June 3, 2008).

     See Appendix A for discussion details and some excerpts.

    Basic principles of the SERNEC Live Plant Image Collection

I. Definitions

     A. SERNEC. Southeast Regional Network of Expertise and Collections.

     B. Photographers. Voluntary participants in the live plant image collection who choose to submit images for the collection. The "photographers" are the copyright holders of the images and may be individuals or institutions.

     C. Users. Individuals or institutions who use images in the SERNEC live plant image collection.

     D. Permanent repository. The Internet-accessible site where high-resolution copies of all images in the collection are archived and made available to users.

     E. Commercial use. Use of images to create a product that will be sold or to promote products that will be sold (i.e. advertising).

II. Goals of the SERNEC live plant image collection

     A. Accuracy.

     1. Inclusion of an image in the SERNEC collection implies that the identification of the image is accurate.

     2. Accuracy in identification will be achieved primarily through the care taken by the photographers. It is assumed that the photographers will have some skill in plant identification or are working with someone with such skills

     3. It is understood and expected that images included in the collection will be subject to annotation by SERNEC taxonomists. The types of images, way that they are photographed, and metadata associated with the images will facilitate verification of the identity of the subject of the images.

     B. Encouraged uses.

     1. Educational use is encouraged.

     a. Noncommercial educational use does not require permission.

     b. Commercial educational use is at the discretion of the photographer but photographers are encouraged to allow low-profit, or not-for profit use at low cost or gratis.

     2. The standardization of images will facilitate the use of many images by different photographers in large-scale educational projects.

     a. SERNEC will facilitate and perhaps coordinate such projects.

     b. Although not required, photographers should be given "courtesy

    notification" of the use of their images in large-scale projects. If possible, an automatic system for accomplishing this may be included in the SERNEC database system.

III. Relationship between the photographer and SERNEC.

     A. Photographers

     1. Photographers retain copyrights to their images unless they opt to release the images into the public domain.

     2. Photographers may continue to use their images as they wish, including publishing them on their own or other websites and making individual arrangements to license them to commercial users.

     3. Photographers agree to license their contributed images under a Creative Commons ("CC"; http://creativecommons.org/) license no more restrictive than Attribution-Noncommercial-Share Alike 3.0 (BY-NC-SA) or to release them to the Public Domain.

     a. The purpose of this requirement is to allow users to use multiple images from the collection for non-commercial personal or educational use without the need to scrutinize the licensing terms of each image.

     b. More restrictive (not allowed) licenses would include any CC license containing the No Derivatives (ND) element.

     c. Less restrictive (allowed) licenses would include: BY, BY-NC, and BY-SA.

     d. In the context of the SERNEC live plant image collection, the Share Alike element is understood to mean that derivative works of the image itself (e.g. images that are cropped, annotated, enhanced, or otherwise modified) created by the user must be licensed under the same license as the original image. The Share Alike element is understood to not apply to other content that may appear with the unmodified image (i.e. on the same web or print page). That other content may be licensed according to the wishes of its creator. (See the comment below about "collective works" in the excerpt from the Creative Commons Frequently Asked Questions.)

     4. Photographers provide metadata associated with the image. These metadata will be organized according to components of the Darwin Core and will include a minimum of taxonomy and photographer data. Optimally they will also include location and other relevant data.

     5. Photographers will follow the established image and metadata standards to the extent that they are able.

     B. SERNEC

     1. SERNEC ensures that submitted images and their associated metadata are archived in a permanent repository.

     2. SERNEC maintains a database of images and their metadata. It provides tools that allow users to locate relevant images in the collection in multiple ways.

     3. SERNEC acknowledges the photographer as the image owner.

     a. SERNEC provides the information necessary for proper attribution of the image.

     b. SERNEC provides a means for the user to contact the photographer (i.e. email or Web address).

     c. The contact and attribution information may be provided through the permanent repository.

     d. SERNEC will attempt to create a means by which users can send a

    blanket "courtesy use request" or commercial use request for multiple images.

     4. SERNEC provides metadata about ID and location to biodiversity projects with the images as photo vouchers. As necessary, the precision of location data are reduced to protect threatened or sensitive populations.

    Excerpt below from the Creative Commons website (http://wiki.creativecommons.org/FAQ) and available under a Creative Commons Attribution 3.0 License

    If I use a Creative Commons-licensed work with other works, do I have to Creative Commons license everything else as well?

    With the exception of those of our licenses that contain the ShareAlike element, the Creative Commons licenses do not require everything else to be Creative Commons licensed as well. We specifically designed the Creative Commons licenses so that they would not turn all other works they were combined with into being Creative Commons-licensed. If you combine any work with a Creative Commons-licensed work that is licensed with a ShareAlike license provision, then, because of the way that the ShareAlike license element operates, the resultant work will need to be licensed under the same license as the original work. If you include a Creative Commons licensed work in a “collective work” (ie. a collection of works in their exact original format, not adaptations), then you only need to continue to apply the Creative Commons license to that work (even if the work was licensed under a Creative Commons Share-Alike license provision). You do not need to apply it to the entire collection.

    Summary of second round of discussion (December 5, 2008)

    Compiled by Steve Baskauf

Live Plant Imaging standards: What do we photograph, how do we

    photograph it, and what kind of information do we want to include with the images?

    I. Considerations:

    A. Purpose. The standards are intended not only to produce standardized orientations of plant parts and to ensure that detailed images are collected of the features that are important for identification, but to facilitate rapid image collection under field conditions and to minimize the need for image manipulation during later processing.

    B. Standardization of views. The development of standardized categories of features to be

    photographed ("views") serves several purposes:

     1. It allows a user to search for similar kinds of images of features from different taxa. The views should be defined in the broadest way that allows functionally equivalent features to come up in a search (e.g. a search for "leaves" should return broadleaf leaves, conifer needles, and fern fronds because they are all functionally leaves vs. defining different views for each).

     2. Minimizing the number of views of a particular feature (leaf, flower, etc.) to a few standardized views decreases the likelihood that images that are really of the same type are not found because their views are described in slightly different ways.

     3. The creation of standardized views provides guidance for photographers so that they know what features are important to be photographed to systematically record the morphology of the plant.

    C. Modifications to images. We are talking about the images that will be archived to serve as raw materials for other uses. We want to preserve the capability for these images to be used for as many other uses as possible. So even though modifications of the images such as creating composites of several features, writing the species name on the image itself, adding borders, etc. may be desirable for some uses, they would preclude other uses and are therefore not appropriate. Such modifications can be made on secondary products (e.g. publications and websites) that use the archive as a source. Likewise, metadata can be recorded in the EXIF data for the image or included in the SERNEC database and therefore do not need to be added to the visual images themselves.

    D. Priorities. Our primary purpose is to provide standards for images that will be used to facilitate species identification and recognition and to be used as an educational resource. If there are competing considerations between these uses and others such as artistic or commercial uses, the educational considerations trump the others.

    II. Standardized views

    A. A set of standardized views should be defined for each major category of plants that have fundamentally different features. At this point (Dec. 2008) the views for woody angiosperms, generic herbaceous angiosperms, and conifers are "mature" enough to be considered as proposed SERENEC standardized views 1.0 . Views for cacti and ferns probably need more work. Views for grasses, sedges, composites, and mosses are needed but have not yet been developed.

    B. Any views that are common to several feature categories should be defined as a single view.

    For example, there should be a single view for bark of a large tree, even though it will be a part of the sets of views for both woody angiosperms and conifers. Thus a non-redundant list of all accepted views will be smaller than the sum of views for all of the major categories. C. List of views.

     1. A list of proposed SERNEC Standardized Views 1.0 is posted at

    http://www.sernec.org/?q=node/213

     2. Collections illustrating the characters have been released on the Morphbank website: woody angiosperms: http://www.morphbank.net/myCollection/index.php?collectionId=464110

    herbaceous angiosperms: http://www.morphbank.net/myCollection/index.php?collectionId=464267

    gymnosperms: http://www.morphbank.net/myCollection/index.php?collectionId=464328

     3. More images illustrating the standardized views are at:

    http://www.cas.vanderbilt.edu/bioimages/image-standards-frame.htm

     4. The standardized views were based on Baskauf, S.J. and B.K. Kirchoff (2008) Digital plant images as specimens: toward standards for photographing living plants. Vulpina 7:16-30.

    http://www.cals.ncsu.edu/plantbiology/ncsc/vulpia/pdf/Baskauf_&_Kirchoff_Digital_Plant_Images.pdf

    D. Based on comments made in the discussion, several changes were made from the standardized views suggested in Baskauf and Kirchoff (2008)

     1. The view of the fascicle base (III.D.2) was very similar to the view of the twig showing attachment of needles (III.C.2) and was dropped from the list.

     2. Seeds are now considered as a separate major category from fruit/cone. This will allow for searches of seed images across the major categories rather than differentiating between seeds from fruits and seeds from cones. Additional specifications or categories for seeds may need to be added after we gain more experience photographing them or receive input from others who already have that experience.

     3. Because many monoecious or dioecious plant taxa have male and female

    inflorescences that differ greatly in appearance, separate subcategories were created for the whole inflorescence subcategory: whole inflorescence (unspecified), whole inflorescence (female), and whole inflorescence (male). Such a split was not implemented for other subcategories of flower views, but that could be considered in the future if enough images of male and female flowers and parts were included in the collection to warrant the split.

     4. There was no clear consensus as to whether a view of the plant in its habitat should be added as a view separate from a general view of the whole plant, so it was not added as a subcategory. If necessary, it could added in the future.

     III. Photographic techniques

    A. Image background.

     1. There was general agreement that distracting backgrounds (e.g. leaves on the forest floor) were not good for close-ups and that out-of-focus or single-color backgrounds were preferable.

     2. In the discussion of image background, there were no compelling philosophical reasons raised for preferring black background over white, although a black background may be easier on the eyes while viewing and more esthetically pleasing. Because it requires no additional work to produce a black background when taking close-ups with a flash, black backgrounds are recommended as the default.

     3. When photographing non-self-supporting objects (e.g. seeds) it is preferable to place them on a black background. High-quality black velvet was recommended. Photographing the

    seeds in situ in the fruit was also recommended. The most important consideration was avoiding a distracting background.

B. Natural light vs. flash.

     1. It was noted that natural light produced more aesthetically pleasing images, but that may not outweigh the disadvantages of hauling around a tripod in the field.

     2. Use of a flash, high shutter speed, and narrow aperture for close-ups provides a long depth of field, little blurring from motion, and a black background.

     3. Due to lack of a clear consensus on this issue, it is recommended that photographers use the technique that seems the most appropriate for the situation.

IV. Metadata collected with the images

    A. Date and time.

     1. Information recorded automatically by camera.

    B. GPS data

     1. GPS data should be collected to document the location of all images.

     2. This can be done manually using a regular GPS receiver, but specialized receivers and software can now embed the GPS data directly into the EXIF information included with the image.

     3. The Darwin Core InformationWithheld element should be used to flag specimens of special concern that should have their GPS resolution reduced to prevent poaching or vandalism. C. Scale information

     1. If the number of pixels per unit length on the object is determined and archived with the image, software can be used to create scale bars or to allow distance measurements on the image.

     2. Using only the distance from the object to the image plane, it should be possible with appropriate calculations to determine the number of pixels per unit length. Photographers should attempt to record this distance (either by reading it off of their lens or estimating it directly). We will work to come up with an accurate method for the calculation.

     3. For the sake of simplicity, the standard unit length should be mm and the distance should be reported in mm.

    D. Taxonomy, location (text), photographer, etc.

     1. Recorded by photographer using any system desired.

    E. Color scale. No opinions were expressed on this topic. Therefore the photographers should simply do their best to adjust the color balance of their images to match the color of the subject.

V. Image and metadata requirements

    A. Meeting the standards. Taking images of all of the suggested views and recording all of the metadata listed is a tall order and probably few if any photographers would actually be able to do so. In addition, some photographers may not want to follow the recommendations listed here. What is the minimum level of conforming to the standards that is required for participation in the SERNEC live plant image collection? We are envisioning a two tier system: a collection of images that meet the full standards and a broader legacy collection that don't meet the full standards.

B. Minimum requirements for images included in the legacy collection:

     1. The specimen is accurately identified to species.

     2. The image can be categorized into one of the standard views and approximately meets the specifications of that view.

     3. The copyright holder (i.e. photographer or institution) is willing to allow use of the image under a license no more restrictive than Creative Commons Attribution-Noncommercial-Share Alike 3.0 (BY-NC-SA). (See notes from previous discussion for more on this.)

C. Preferences for images included in the legacy collection.

     1. Images from the same specimen are associated with each other.

     2. Text location data (DwC Continent, Country, StateProvince, County, and Locality elements) provided.

     3. High resolution image of at least 3 megapixels provided.

D. Minimum requirements for images included in the regular collection.

     1. Images of enough views are taken of the specimen to allow for identification and annotation from the images. Images of the same specimen are associated with each other. The more views taken the better, but we recognize the time limitations of the photographer. The Baskauf and Kirchoff (2008) paper suggests which views are the most important to photograph. The specimen is accurately identified to species.

     2. The image can be categorized into one of the standard views and meets the specifications of that view.

     3. Text and GPS location data provided for the specimen. DwC InformationWithheld element should be used to flag sensitive species for which the GPS data reduced in resolution.

     4. Date and time information are available in the EXIF data associated with the image.

     5. The copyright holder (i.e. photographer or institution) is willing to allow use of the image under a license no more restrictive than Creative Commons Attribution-Noncommercial-Share Alike 3.0 (BY-NC-SA). See previous discussion for more on this.

     6. High resolution image of at least 3 megapixels provided.

     7. No distracting objects in image and no text added to image. No collages.

E. Preferences for images included in the regular collection.

     1. High resolution image of at least 6 megapixels provided (all new images should be taken with this as a minimum resolution).

     2. Background of close-ups black.

     3. Distance from object to film plane in mm provided (to establish scale).

     4. If the photographer is working in a team collecting physical specimens and the photographed plant is actually collected, the catalog number of the physical specimen should be associated with the images.

     G. How the collection designations will be used.

     1. A user who is just looking for images that illustrate a particular feature in a particular species, or who wants to see a number of images from a particular species would conduct a search of images in the set containing the legacy + regular collection.

     2. Users who want to develop resources in which standardization is important (keys, learning tools, etc.), who want to access occurrence records (e.g. GBIF or Flora of the Southeast), or who want to examine the variation in morphology among specimens would restrict their

Report this document

For any questions or suggestions please email
cust-service@docsford.com