Calcification metrics in CoralNet

Quantifying coral reef benthic community composition is not the only way to evaluate coral reef health. Another important metric is the net accumulation of carbonate production, which provides valuable insights into how the geo-ecological functions of coral reef structures may change in the future.

CoralNet provides a way to estimate coral reef carbonate production over a source's images. By counting how much of each label is present in a dataset and assigning calcification, microbioerosion, and macrobioerosion rates to each label, we can compute the overall estimated rate of carbonate production for that dataset.

Label calcification rates provided by CoralNet

Because quantifying site-specific calcification, macrobioerosion, and microbioerosion rates represents a significant challenge, CoralNet provides default rates for many commonly used labels in either the Atlantic or Indo-Pacific regions. These rates are based on an area-normalized scaling of calcification, microbioerosion, and macrobioerosion rate data from ReefBudget. For additional details on the development of these rates for CoralNet including the methodology, code, and data inputs, please see the associated code and data release here on GitHub.

In addition to the verified (and duplicate) status indicators, CoralNet's label list page will show a blue 'C' when a label has calcification, microbioerosion, or macrobioerosion rates provided by CoralNet.

The label detail pages show what the CoralNet-provided rates are, and for what regions. Some labels may have rates defined for one region:

Some may have rates defined for multiple regions:

And some may have no rates defined by CoralNet:

Also, when adding/removing labels to a labelset, there is an indicator of rate availability in the popup for each label:

Note that the "Available" indicator here, as well as the "C" on the label list, will show when rates are available for at least one region. The indicator does not necessarily mean that rates are available for all regions.

Exporting per-image calcification rates

Things you must do in your source first:

  • Create a labelset.
  • Upload some images.
  • Annotate some images.

Once you've done that, you can export calcification metrics for your source. First go to your source on CoralNet and click "Images" at the top.

If you want to export data for a subset of images in your source, rather than all images, use the search fields to specify the subset of images you want, then click Search.

Scroll down to the "Image Actions" box. You must be signed in to see this box, even if the source is public.

Select "Export" in the first dropdown, and then "Calcification Rates" in the second dropdown.

In the third dropdown, select whether you want to export this data for all images in the search, or just for the images on this page of results (can be useful as a test run).

Here's an example to demonstrate how the per-image carbonate production estimates are calculated:

  • Suppose an image has 10 points. 5 CCA, 3 Porites, 2 Acropora.
  • Suppose those three labels' mean calcification rates are taken to be 0.4, 7.2, and 18.0 kg CaCO3 m-2 yr-1 respectively.
  • The image's estimated net carbonate production rate (kg CaCO3 m-2 yr-1) is then: (5*0.4 + 3*7.2 + 2*18.0) / 10 = 5.96

The exported CSV/Excel file contains carbonate production estimates for each image, and then a summary row at the end which averages rates over all the images.

If you choose the Excel option, the Excel workbook will contain multiple worksheets: one for the per-image rates, one with meta information about the export, and one with a copy of the label-rates table that was used.

For more details on the export form, click the "?" button and read the "Calcification Rates" section of the help text.

When you are ready to export, click "Go" and wait for your .csv or .xlsx export file to be generated. This may take a few minutes, and you must stay on this page until the export file is generated. Once it has finished generating, your browser will start downloading the file (or will prompt you to choose a download location).

About label rates

When choosing the label-rates table (the "Label rates to use" field), there are two main considerations:

  • You want the label-rates table to cover as much of your labelset as possible. If a label does not have a rate defined, CoralNet will assume a rate of 0 (no net calcification or bioerosion) for that label when computing per-image rates, which may make these computed carbonate production rates inaccurate.

  • You should choose the label rates which are most accurate for your source's data. Some labels have rates defined in both the Atlantic and Indo-Pacific tables provided by CoralNet, but if your dataset is based in the Pacific Ocean, then you should use the Indo-Pacific table to get the most accurate rates.

If CoralNet's provided rate tables aren't sufficient for your source and/or you prefer to upload your own site-specific rates, you can upload your own table. First click "Click here to manage label-rate tables", then click "Download CSV (labelset entries only)" for any of the tables. This will let you download a template rate-table with one row per label in your labelset.

You can then edit this CSV file, replacing the zeros and any other rates with your own rates. If editing with a spreadsheet program like Excel, make sure to save your edits in CSV format. Then, click "Upload a new table" and use the form there to upload your edited rates.

You may save up to five custom rate tables for a source. If you want to upload a new table and you already have five tables, you must delete one of the previously uploaded tables first.

Different tables for different images

If you happen to have a source that spans multiple biogeographic regions (e.g. with some data from the Atlantic and some from the Indo-Pacific), you may want to do multiple export operations. Export one CSV/Excel file for a subset of images with one table, then export another CSV/Excel file for the rest of the images using a different table. Then to get a source-wide summary, you'll have to combine the metrics from those CSV/Excel files yourself.

Remember that you can use the auxiliary metadata fields (up to five) to filter your images any way you want. Go to Admin -> Edit Source Details to name the fields:

Go to Metadata (or Upload -> Upload Metadata) to set metadata values per image:

Then go to Images, specify metadata values to filter to, and click Search.

Then proceed to export estimated carbonate production rates for your images.

Note: In general, CoralNet sources are usually limited to one geographic location, though there's no rule that prevents you from populating a source with data that spans multiple regions. Of course, if there is any other reason for you to export metrics for only a subset of your images, the above procedure applies as well.