Be a Marine Scientist! Using FathomNet Portal for Species Identification
- Deanna Soper
- Jul 29
- 5 min read
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What is FathomNet Portal?
FathomNet is a community-driven research and development program that aims to accelerate understanding of ocean life by identifying marine organisms in underwater imagery. Led by partners at MBARI, Ocean Discovery League, CVision, and CeNCOOS, the FathomNet program connects machine learning data analysis tools with a spectrum of users, from experts to enthusiasts. FathomNet has developed three core solutions—Portal, Database, and FathomVerse—that combine state-of-the-art technology and community power to build an unprecedented resource for the ocean. By standardizing marine image data and making them widely accessible, FathomNet advances scientific understanding of marine ecosystems while supporting education, conservation, and autonomous underwater technologies.
The FathomNet Portal is an online, collaborative tool for end-to-end AI-assisted processing of ocean imagery. Via a web interface, Portal users can access AI models and create annotations to analyze their videos and photos of the ocean.
In previous exercises, you have explored the FathomVerse application and the FathomNet Database to build foundational skills in marine species identification. In this section, you will take the next step by learning to use the FathomNet Portal. The Portal enables users to import images and videos, identify organisms, and create detailed annotations. While images and videos provide valuable observations of marine organisms, they do not automatically generate searchable scientific datasets. To make these observations useful for research, annotations must be created to identify organisms and record important contextual information. In the FathomNet Portal, this process involves localizing organisms by drawing bounding boxes (See Figure 1) around individuals and assigning the appropriate taxonomic identification. These localizations allow researchers to quickly locate and review organisms of interest while simultaneously creating data that can be used to train machine-learning algorithms. Ultimately, these algorithms will be used to generate suggestions for species ID. But to get to that point, datasets need to be large. Recently, marine scientists have focused on expanding the datasets by using tools such as the FathomNet Portal. As the AI models improve, researchers will be able to analyze large volumes of ocean imagery more efficiently, accelerating discoveries about marine biodiversity and ecosystem dynamics.
Assignment
This lab will introduce the core tools and functions of the FathomNet Portal and guide you through the annotation process and best practices for accurate species identification. By the end of this exercise, you will understand how your annotations contribute to real-world scientific research and the advancement of AI-assisted marine exploration.
Using the provided project folder, create accurate localizations and annotations for each assigned organism. Follow the instructional video below to learn the annotation workflow and use the provided annotation reference list to correctly identify each observation. Draw precise bounding boxes around organisms and assign the appropriate taxonomic label. Verify your annotations with the course instructor to ensure accuracy and consistency.
Instructions
Log into the FathomNet Portal at portal.fathomnet.org using the username and password provided by your instructor. Once logged in, confirm that you have successfully accessed the correct workspace before proceeding.
Locate your assigned project folder, labeled “FathomNet Education,” on the left-hand side of the dashboard. Within this folder, you will find video files labeled 1–15, which contain the organisms that you will be identifying and annotating.
Open the spreadsheet titled “FathomNet Portal – Taxonomic Key.” When you open the spreadsheet, you will be prompted to copy it to your own Google Drive. Review the organisms labeled A–O. This spreadsheet serves as your reference guide and will be used to match each organism with its corresponding video segment.
Research each organism using the FathomNet Database, NOAA’s Benthic Deepwater Animal Guide, the World Register of Marine Species (WoRMS), and other approved scientific resources your instructor might give you. Your goal is to determine the most specific taxonomic classification possible. Species-level identifications are preferred; however, if you cannot confidently identify the organism to species, work backward using the taxonomic key linked above until you reach the rank that can be supported by the available evidence.
Using the information gathered from your research, match each organism listed in the Taxonomic Key with its corresponding numbered video file from the provided files. Continue this process until all organisms labeled A–O have been paired with the correct videos.
Open a numbered video file and review the footage until you locate a clear frame containing the target organism. Whenever possible, select a frame that provides an unobstructed view of the entire organism and minimizes blur, shadows, or visual obstructions.
Select the “Create a box annotation” tool located in the toolbar at the top of the Portal. Using this tool, draw a bounding box that completely encompasses the organism while minimizing unnecessary background space. Ensure that no part of the organism extends beyond the boundaries of the box. Again, use the instructional video above as a guide to creating an annotation.
Enter the most specific taxonomic identification that you can confidently determine in the “Observation” field. Verify the accuracy and spelling of the taxonomic name before continuing.
Review the annotation to ensure that both the bounding box and taxonomic identification are accurate. In the "Notes" section, enter the organism's label as listed in the Taxonomic Key (e.g., "Organism A"). Once you have confirmed the information, select “Save” to record the annotation within the Portal.
Repeat this process for all remaining organisms until each organism labeled A–O has been correctly identified, matched to a video segment, and annotated in the FathomNet Portal. Before submitting your work, perform a final review to ensure that all annotations are complete, accurate, and consistent with the assignment requirements.
Assessment
After confirming the accuracy of your annotations, complete the "Segment Number" column in the "FathomNet Portal – Taxonomic Key" spreadsheet. Each organism A–O corresponds to a single video segment, and no video segment will be used more than once. Submit the completed spreadsheet by the end of the lab period.
Prior to the next lab session, upload the original image or video from your Deep Sea Scientific Illustration lab or any other image or video you might find on a publicly available source, such as NOAA’s Benthic Deepwater Animal Guide, to the shared FathomNet project folder labeled "Upload Images." This exercise is intended to familiarize you with the Portal's media upload process. Follow this instructional video to ensure that your media is uploaded correctly. This uploaded media will serve as the basis for future annotation exercises and provide additional experience working with the FathomNet Portal workflow.
How to upload media to the FathomNet Portal Finally, properly annotate your uploaded media as you practiced during the lab. Either share your link with your instructor, or if your instructor wishes, you can download a CSV file by going to Observations → Filter → Modified by = “NAME” → Download Data (CSV).
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