Importing CoralNet data into MERMAID

Have photo quadrat data annotated in CoralNet? You can import these directly into MERMAID using Easy PQT to have all your data in one platform.

Steps to import your CoralNet data to MERMAID

Step 1: Prepare your project in MERMAID Collect

Before importing data, your project needs to be set up in MERMAID Collect:

• Set up a new project (or check that you have an existing project ready for the data import):

  • Add your organization(s).

  • Add users and assign their roles.

  • Set data sharing policies.

  • Add sites and management regimes associated with the data you are importing. 

Read more in Setting up a project.

Step 2: Export Data from CoralNet

Export your data from CoralNet using the steps below:

• Make sure you are using the auxiliary fields that include: Site, Management regime, and Transect number (names can be customized). If you haven’t used the auxiliary fields, you need to set them up in your CoralNet project (more info on how to add auxiliary fields can be found in the Calcification Metrics in CoralNet help page under the Different Table for Different Images section.

• Navigate to your CoralNet project > Images > Image Actions > Export Annotations, CSV.

• Select the label format Both to include the short codes and ID numbers. MERMAID will refer to the ID numbers to assign the right MERMAID benthic attribute and/or growth form for each of your labels.

• Include optional columns: Image metadata – date and auxiliary fields.

Step 3: Open MERMAID Easy PQT

• Navigate to the MERMAID Easy PQT

• Easy PQT will prompt you to authenticate using your MERMAID credentials.

• After login, choose CoralNet as the provider you used to annotate your photos, then a list of your eligible (non-test) projects will be displayed under MERMAID Project.

Step 4: Upload exported file

• Select the project you want to import your data into.

• Upload your file by clicking Browse or drag and drop your file into the upload modal. Only a CSV file exported from CoralNet will be readable by Easy PQT.

Step 5: Match auxiliary fields

• Match your CSV’s auxiliary columns with Site, Management, and Transect values in your MERMAID project.

• Easy PQT will validate your entries and highlight any mismatches with guidance.

Step 6: Assign CoralNet labels to MERMAID benthic attributes

• MERMAID Easy PQT automatically assigns CoralNet labels to MERMAID benthic attributes and/or growth forms.

• Any unassigned values appear in red at the top of the table. Click and type or use dropdowns to assign the correct benthic attribute and/or growth form.

Once all of your labels are assigned and reviewed to valid MERMAID benthic attributes, you can click the “Confirm” button to continue the importing process.

Step 7: Review and import data into MERMAID

• Once your data is reshaped and validated, click Import data.

• Alternatively, you can restart by clicking on the Restart Easy PQT button or get help by clicking on the Get Help button if something doesn't look right.

• You can also download the reshaped dataset as a CSV by clicking the “Download reshaped data” button on the top right of the table.

• Once the importing process is complete, you’ll receive a confirmation message on your screen: Import successful! 

• You can either close the window or scroll to the bottom and click on Go to MERMAID Collect to finalize the import process in MERMAID Collect. 

Step 8: Complete sample units in MERMAID Collect

• Go to your Collecting page in your project.

• Complete required fields: depth, transect length, and quadrat size.

• Verify observer info. MERMAID will automatically assign you as the observer. You can change the observer if someone else collected the data.

• Validate each individual sample unit.

• Submit each validated sample unit.

• Once submitted, sample units become available to all project’s users in the Submitted page.

Do you prefer a code-based workflow in R?

For R users, see Importing Legacy Data into MERMAID.