DendroElevator (DE) is a collaborative effort that links the Griffin Lab, AISOS, and LATIS, with emphasis on student-centered imaging technology and software development for research, education, and outreach. DE combines browser-based tools for developing measurement time series with a potent cloud-hosted digital curation platform.
The current generation of DE relies heavily on leaflet, an open-source javascript display plugin. Leaflet-treering is our open-source, browser-based toolkit for tree-ring measurement, dating, and annotation that leverages WebGL for advanced image visualization.
Elevator is an open-source, cloud-hosted digital asset management platform developed by Colin McFadden, a technology architect in the College of Liberal Arts at the University of Minnesota. More information is available through the elevatorapp.net page and the related repository on GitHub.
As of November 2022, DE hosts over 10,000 image assets for dozens of lab groups across more than ten academic and governmental institutions.
Basic end user access to DE requires only a modern web browser and moderately reliable internet connection.
BACKGROUND
DendroElevator is cloud-native software for basic dendrochronology, optimized for modern imaging approaches.
DendroElevator works with digital image files of most formats and any file size. Image assets are organized into project or site-level collections, which are nested within institutional and lab group collections, where access privileges are set for user groups, which are composed of specific individual end users. Ultimately, end use requires only a modern web browser, access to basic internet, and some basic familiarity in tree-ring wood anatomy and micrometry.
This open-source cyberinfrastructure project is intended to support the communities of scientific researchers that produce data from tree rings, aquatic organisms, and related environmental proxy types. Basic access to dendro.elevator.umn.edu is open to any such researchers. The platform uses AWS, and does come with costs for digital image data file storage and streaming. As of November 2022, the platform remains in an incubation phase at the University of Minnesota. As data volumes grow, we expect that user groups with large data volumes may be expected to cover reasonable costs of storage and streaming for their data.
Inquiries about individual and user group account access should be directed to Daniel Griffin (griffin9@umn.edu).
ADDING DATA
Users wishing to add assets to Elevator are advised to
provide a csv with metadata where headers match exactly those in this file.
Note that this is the only time metadata can be edited in bulk, and once assets are created, metadata must be updated on an individual basis.
Provide the name of the collection where these assets will be created (can be an existing or new collection).
Users are encouraged to use the following convention of institution>lab group>Site code, country-state, species, site name
UMN>Griffin Lab> LKR | US-WI | QUMA | Lower Kinnickinnic River
Site admin (Currently Griffin) will create collections and assets by uploading csv (Admin required), and pending permissions status, individual users can then edit assets to upload their individual image files. Permissions are generally organized around institutional lab groups.
MORE INFORMATION
Digital Assets are the fundamental digital object unit in Elevator. Any data file type can be uploaded to and attached to an Elevator asset. Plugins are embedded to enable users to visualize/interact with many common data file types (pdfs, images, videos, etc.). It is possible to associate multiple digital files of various types with an individual asset.
The leaflet-treering plugin at the core of DendroElevator is only capable of creating one single measurement time series per asset. So each growth radius (increment core, or measurement path on a cross section) should have its own asset. For a core or cross section where multiple paths will be created on a single image, the image can be uploaded to as many assets for which there are intended measurement paths.
Collections are the primary unit of organization for assets in Elevator. Collections can be nested, so most collections are either the parent or child of another collection. In DendroElevator, collections are currently organized by institution (e.g., UMN), lab group (e.g., Griffin Lab). For example, the “LKR | US-WI | QUMA | Lower Kinnickinnic River” collection is nested within the parent “Griffin Lab” collection which is nested within the parent “UMN” collection, which has no parent. The resulting path within elevator would be “UMN>Griffin Lab> LKR | US-WI | QUMA | Lower Kinnickinnic River” or similar. Only Elevator instance administrators can create collections, and modify their nesting/dependency on other collections and permissions.
Permissions in Elevator are set for user groups, which are comprised of specific individuals. Typically, a user group is made for an institutional lab group (e.g., UMN Griffin Lab), and then that group of individuals is given permission to add/edit/delete assets and save measurement data to the cloud in .json format for all of the collections nested within that user group’s collections.
Adding new assets to Elevator is easiest for bulk creation using the csv upload function, which is currently only available to the administrator (Griffin, in this case). The csv import creates one asset per row, and text in the “Specimen ID” column will become the default name of the individual assets. Note that this is the only time metadata can be edited in bulk, and once assets are created, metadata must be updated on an individual basis.
New assets can be added to existing collections any number of times. Assets can be moved to a different collection later, also on an individual basis. A collection can include assets with different metadata templates.
Individual users can create and edit individual assets, entering metadata into its related web form.
When created, each asset must use an Elevator metadata template, and each asset must be assigned into an existing collection. We are currently using the template “DendroMetadata,” which is occasionally updated and can be expanded as needed. Currently, in DendroElevator, the metadata template includes fields that match the header names in this example.
Access Permissions Hierarchy
Permissions to view/add/edit/download assets in Elevator are set by the administrator (in the case of DendroElevator, currently Griffin), who assigns individual users to specific user groups, and then sets the user group permissions for a given collection. User group permissions cascade into nested collections. For example, if an individual named “Student 1” is added to the user group “Griffin Lab Users” and that user group can add/edit/download assets in the collection “Griffin Lab,” that individual will have those permissions for any collection nested within.