Downloading Data & Export Packages

Portal is an ideal location for users wishing to curate, and stage their data for other systems, including the FathomNet database.

Exporting From the FathomNet Portal can be done in a few ways based on the user's needs. At the time of this tutorial there is one export packaged defined for the FathomNet Database Export, and in the future the FathomVerse game and other export types will follow.

Downloading Data

A basic and direct way to download your information from portal to your personal computer, is from the Observations Gallery using the link to download the data as a CSV. The downloaded file contains information relating the observations in the selection. In portal, observations are tracks, and can be a single or multiple localizations grouped to identify a sinlge animal travelling through time, for example. These quick-summary downloads present the observation-level information including the classification, and the box information and sensor data (if any) related to the first frame of the Observation. The file is downloaded immediately and saved in CSV format.

Export Packages

Export Packages are slightly different in that the are a way to share references to images or frames at a particular point in a video with outside sources, or for further research or model training.The first export package available is a CSV file formatted for submission to the FathomNet Database.

The first step is to mark frames and/or images from your project for export. Marking for export puts the frames/image into a staging area where they can be validated and assembled into an export package. Read more about marking for export here. Once the staged items are ready, their staging area may look like the screenshot below. The Staging Area can be accessed from any tab at the folder or project level, all of the selected frames or images will be shown with localizations drawn on top.

You will notice that the export staging area is frame-based in view. Once an export is created, the portal will publicly host an image for each of these frames. The public public url can be used to fetch the image from external sources and will be used a reference for each localization drawn on them in the gallery.

Clicking "Export for FathomNet" begins the process. The following modal allows you to name the export, and you are emailed after the backend process completes, a CSV file will be emailed to you. The attached CSV formats your portal data and attributes into rows and columns readable by the the FathomNet database.

Submission to FathomNet Database

From there you currently will go to FathomNet Database to complete the submission. There are more detailed instructions for this on the FathomNet Medium blog: https://medium.com/fathomnet/how-to-submit-localized-image-annotations-to-fathomnet-baf25dbd8165