We’re excited to announce two new features in VisualSpreadsheet 6 to support data management and exporting data to EcoTaxa, a collaborative web-based platform for classifying and validating plankton images.
This update is especially valuable for plankton researchers craving new ways to organize and search for data in VisualSpreadsheet and/or a streamlined way to format and export data for EcoTaxa.
What is EcoTaxa, and why is it valuable for FlowCam users?
EcoTaxa is an open-access, collaborative platform that enables users to upload, classify, and validate plankton images from a variety of plankton imaging instruments. EcoTaxa is valuable because it enables users to:
- Make data publicly available
- Invite multiple people to work collaboratively on the same dataset in real time
- Use machine learning to support image classification
- Explore data from multiple plankton imaging instruments using a single interface
- Open and classify multiple samples at once
For FlowCam users, EcoTaxa provides a way to share plankton image data between collaborators. It helps researchers contribute to large-scale ecological datasets and access powerful classification tools without having to build custom models.
Summer plankton community in Casco Bay, Maine. EcoTaxa training project with validated FlowCam images. Taxa include ciliates, diatoms, dinoflagellates, shellfish larvae, and other marine plankton.
Interested in exploring an example project in EcoTaxa? First login or create an EcoTaxa account, then click here to check out an example project.
What's new in VisualSpreadsheet?
Traditional pathways for getting FlowCam data into EcoTaxa require raw camera images and segmentation using Zooprocess. However, most FlowCam users don’t have raw camera images because they take up so much space and reduce sampling efficiency.
To help support users who want to use EcoTaxa, previous updates to VisualSpreadsheet 6 enabled users to automatically export individual particle images (aka vignettes), and some users wrote code to format particle data (e.g. FlowProcess).
In VisualSpreadsheet 6.1, we’re taking it a step further by making it possible for users to export vignettes, particle data, and metadata in the format EcoTaxa requires without having to leave VisualSpreadsheet.
Adding metadata to FlowCam runs
One of the most powerful aspects of the new VisualSpreadsheet 6.1 release is the ability to create and apply metadata tags to FlowCam runs. While this feature was designed to support EcoTaxa compatibility, it also provides lasting value for any FlowCam user interested in new strategies to make FlowCam data more structured and searchable.
With metadata tags, users can capture essential context about each sample, such as project name, sampling station, sampling depth, preservation method, and environmental parameters. These tags make it easier to filter, sort, and organize data within VisualSpreadsheet, ensuring that important details about sample origin or processing always follow your images. For oceanographic transects or long-term monitoring projects, metadata tags can provide critical traceability, helping researchers link imaging data back to the original sampling conditions.
VisualSpreadsheet provides a list of default metadata tags, including fields like date, time, and coordinates that are formatted for EcoTaxa, but also allows you to create your own tags, allowing you to tailor your data to the specific needs of your study and your lab—an especially useful feature when a single FlowCam instrument is used for multiple projects. Metadata fields are also searchable, making it easier to find specific datasets and to apply best practices for managing image data.
How to export FlowCam data for EcoTaxa
We’ve created a step-by-step technical note that walks you through the full process, including how to customize metadata tags, build EcoTaxa report templates, and export FlowCam data to EcoTaxa.
Whether you’re monitoring harmful algal blooms in coastal waters or studying seasonal plankton dynamics in inland lakes, VisualSpreadsheet 6.1 offers new features for users to organize their data and export it to EcoTaxa so that you can spend more time working with your data, rather than wrestling with how to format it.
Download the Technical Note:
Using VisualSpreadsheet to Create Metadata Tags and Export Data to EcoTaxa
