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Add context about images #427

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Dec 7, 2023
Merged

Add context about images #427

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7af4347
Add context about images
themerekat Dec 6, 2023
ef6897d
Change order of images tabs
themerekat Dec 6, 2023
b80e89a
Re-write batch upload instructions
themerekat Dec 6, 2023
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19 changes: 13 additions & 6 deletions content/coll_manager/images/_index.en.md
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@@ -1,19 +1,31 @@
---
title: "Images"
date: 2021-10-06
lastmod: 2023-12-06
weight: 80
draft: false
authors: ["Ed Gilbert","Katie Pearson"]
editors: ["Katie Pearson"]
keywords: ["images"]
---

{{< notice info >}}
This page describes the types of images that are available through Symbiota portals.
{{</ notice >}}

Images may be associated with records in Symbiota portals by storing links to those images in the database tables. If a Symbiota portal is configured to accept images (i.e., image storage at the institution that hosts the portal is allowed), those image links may be generated by the portal. Storage of a large number of images on servers associated with a Symbiota portal (e.g., at Arizona State University) may require an image-hosting agreement and/or incur image-hosting costs. Check with the portal administrator for more information about your portal's image hosting allowances. Otherwise, tools are available to link external URLs to occurrences by matching on catalog numbers.

To watch a helpful webinar on how images are managed in Symbiota portals, <a href=https://youtu.be/v2bcx4oKDVI target=_blank>click here</a>.

There are three categories of images that can be linked to a Symbiota portal:

{{< tabs >}}
{{< tab "Occurrence (Specimen) Images" >}}
Images of physical specimens should be linked to their respective specimen records. Specimen images are available both from the Occurrence Details page and the Taxon Profile page for the taxon associated with the most recent determination. If the specimen identification is annotated, the identification of the image will be automatically re-mapped to that taxon. Specimen images can be added through the Occurrence Editor or in batch via multiple processes.
<br><br>
See <a href=https://biokic.github.io/symbiota-docs/editor/images/upload/>Uploading Images</a> for more details.
{{</ tab >}}

{{< tab "Field Images without Location" >}}
Images without specific locality information (e.g. lat/long coordinates) are linked only to the scientific name of the organism. These images can be viewed through Taxon Profile Pages, which have general information such as descriptions, distribution maps, synonyms, and common names. Field images are uploaded and managed through the Taxon Profile pages by users with Taxon Profile editing permissions. Field images with specific locality details (e.g. coordinates) can be loaded as Image Vouchers (see "Field Images with Location" tab). See <a href=https://biokic.github.io/symbiota-docs/editor/images/upload/>Uploading Images</a> for more details.
{{</ tab >}}
Expand All @@ -24,10 +36,5 @@ There are three categories of images that can be linked to a Symbiota portal:
Image Vouchers are displayed on both the Occurrence Details and the Taxon Profile pages. Image-supported observations can be uploaded using the Observation Submission page. Up to three images can be submitted for a single observation. Data fields required for an image to qualify as a voucher include: observer name, observation date, country, state, locality description, latitude, longitude, and at least one image. Contact your data portal administrator for information on whether observations are allowed and the necessary protocols for submitting an observation. Some portals require the review of a tutorial before one is authorized to submit an observation.
See <a href=https://biokic.github.io/symbiota-docs/editor/images/upload/>Uploading Images</a> for more details.
{{</ tab >}}

{{< tab "Specimen Images" >}}
Images of physical specimens should be linked to their respective specimen records. Specimen images are available both from the Occurrence Details page and the Taxon Profile page for the taxon associated with the most recent determination. If the specimen identification is annotated, the identification of the image will be automatically re-mapped to that taxon. Specimen images can be added through the Occurrence Editor or in batch via multiple processes.
<br><br>
See <a href=https://biokic.github.io/symbiota-docs/editor/images/upload/>Uploading Images</a> for more details.
{{</ tab >}}

{{</ tabs >}}
23 changes: 15 additions & 8 deletions content/coll_manager/images/batch/_index.en.md
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---
title: "Batch Uploading/Linking Images"
date: 2021-10-06
modified: 2023-10-17
modified: 2023-12-06
weight: 1
authors: ["Ed Gilbert","Katie Pearson"]
editors: ["Katie Pearson"]
keywords: ["images"]
---

{{< notice info >}}
This page describes how to upload multiple images at a time or link multiple images from an external location.
This page describes general workflows for adding multiple images to a portal at one time. Technically, images are not stored within a Symbiota database. Instead, the URLs of the images are mapped to specimen records. Contact the portal manager to inquire about the workflows supported by a given portal.
{{</ notice >}}

There are several workflows used to batch upload/link specimen images. Batch processing typically consists of two separate steps: 1) Batch loading images onto a web server, and 2) Mapping image URLs to specimen records residing within the Symbiota portal. Technically, images are not stored within a Symbiota database. Instead, the URLs of the images are mapped to specimen records. Contact the portal manager to inquire about the workflow details supported by a given portal.
Images associated with records in a Symbiota portal may be **Externally Hosted** or **Internally Hosted**.

* **Externally Hosted** images are those stored on servers that are unrelated to the Symbiota portal (e.g., are housed at another institution). These external servers provide image links, which can then be loaded into the Symbiota database.

* **Internally Hosted** images are those stored on servers that are write-accessible to the Symbiota portal server. For example, if you coordinate with Arizona State University to batch upload images to one of their hosted portals (e.g., SEINet, Bryophyte Portal), your images are Internally Hosted.

{{< notice tip >}}
Images uploaded or linked to specimens in a Symbiota portal should be JPGs or in another web-friendly format. It is recommended that individual files are no larger than 8 MB to allow users with slower connectivity to view them within a reasonable timeframe.
{{</ notice >}}

### Common Workflows
* **Image Drop Folder:** Using a mapped network drive, FTP, SFTP, Dropbox, or other cloud storage, a drop folder is made available so that the imaging team can regularly deposit new images. This folder is referred to as the "source folder". Once images are uploaded to the source folder, you can use the Processing Toolbox to create web-ready derivatives and move the images to a local server. The derivatives are then mapped to specimen records through image URLs.
#### Batch Adding Externally Hosted Images

Externally Hosted images can be added to Symbiota records using one of three primary methods: (1) using the URL mapping tool and a spreadsheet of catalog numbers with image URLs (documentation coming soon!); (2) mapping a column of image links to the associatedMedia field when conducting a Full Text File Upload or Skeletal File Upload. For more information about uploading text files, see <a href=https://biokic.github.io/symbiota-docs/coll_manager/upload/>this page</a>. If you already have data in the portal, and you just want to add image links, do NOT use Full Text File Upload; or (3) importing a Darwin Core Archive of your data with a fully-populated <a href=https://rs.gbif.org/extension/gbif/1.0/multimedia.xml target=_blank>multimedia extension</a>.

#### Batch Adding Internally Hosted Images

* **Local Storage:** If images are stored on a local server that is write-accessible to the portal code, image processing can be performed directly through the portal interface. Image URLs stored locally can be mapped into the database using relative links without the domain name. In this case, the the web server user (e.g. Apache user) must have write access to both the source and target folders.
There are several workflows used to batch upload/link internally hosted specimen images. Batch processing typically consists of two separate steps: (1) Loading images onto a web server, and (2) Mapping image URLs to Symbiota occurrence records. Step (2) is possible when images are named according to the catalog number or other catalog number associated with the record in the portal.

* **Remote Image Storage:** Images can also be processed and stored on a remote server and mapped to the specimen image through the full image URL. Standalone image processing scripts will be needed to process images and map image URLs to the portal database. Scripts can be configured to write the image URL directly to the database or image metadata can be written to a log file, which is loaded into the database afterwards. Remote images must be mapped into the database using the full image URL with the domain name.
* If only a large image is made available from the remote server, the image URL can be mapped to the _urloriginal_ field, and then portal will then create local web and thumbnail dirivatives. If the images are named using the catalog number, and the web server is configured to display directory contents, the Processing Toolbox within the collection's management menu contains a method to harvest image links from the directory listing. Alternatively, one can perform a "skeletal record import" that contains a column with the catalogNumber and another associatedMedia column with the image URL.
Storage of a large number of images on servers associated with a Symbiota portal may require an image-hosting agreement and/or incur image-hosting costs. Check with the portal administrator for more information about your portal's image hosting allowances and workflows. For ASU-hosted servers, contact the Symbiota Support Hub ([email protected]).