Using EcoTaxa with FlowCam
EcoTaxa is a free, online platform for collaborative prediction and validation of plankton images from instruments like FlowCam. This page is a one-stop shop for resources developed and curated by the FlowCam team to support the success of FlowCam users interested in using EcoTaxa.
FlowCam Customers: Click here to access these resources in the Customer Support Center
Background
EcoTaxa, developed by the Quantitative Imaging Platform of Villefranche (PIQv), helps researchers classify and validate plankton images.
Over the years, FlowCam users have adopted a variety of workflows to prepare data for EcoTaxa, ranging from raw image processing in Zooprocess to custom scripts developed by the user community.
In response to user requests, the FlowCam team introduced a streamlined workflow to help users export EcoTaxa-ready data from VisualSpreadsheet 6.1 without requiring raw images or coding experience.
The resources on this page will help you learn about EcoTaxa, determine its suitability for your research, and get started using the new VisualSpreadsheet 6.1 pipeline.
Whether you're new to FlowCam and EcoTaxa, an experienced user, or somewhere in between, this page offers resources for users interested in adding EcoTaxa to their image analysis toolbox.
1. EcoTaxa Background
Webinar: Introduction to Quantitative Plankton Imaging & EcoTaxa
Meet Dr. Fabien Lombard from the Quantitative Imaging Platform (PIQv) at Laboratoire d'Océanographie de Villefranche (LOV) in France where EcoTaxa was developed. In this webinar, Dr. Lombard presents the opportunities and challenges associated with quantitative plankton imaging and explains why his lab developed EcoTaxa to handle large datasets from long-term monitoring sites and oceanographic expeditions.
Related Resources:
From Sample to Insight with FlowCam and EcoTaxa: This blog post summarizes the webinar—check it out!
EcoTaxa Training in Villefranche-sur-Mer: Read about our team’s trip to Villefranche-sur-Mer for training.
2. Preparing VisualSpreadsheet 6.1 Data for EcoTaxa
Technical Note: Using VisualSpreadsheet to Create Metadata Tags and Export Data to EcoTaxa
Webinar: How to Use FlowCam's New EcoTaxa Friendly Features
Learn how to use VisualSpreadsheet 6.1 to add metadata to your runs and export images and metadata in an EcoTaxa-ready format. Read the technical note and watch the supplementary webinar to see how it’s done.
Related Resources:
From FlowCam to EcoTaxa: New Features Make Data More Accesible: Check out this blog post for a quick summary of the themes addressed in the webinar.
3. Getting Started in EcoTaxa
Webinar: Getting Started with EcoTaxa for FlowCam Users
Ready to start using EcoTaxa? This webinar, designed for beginners, walks through key functions in EcoTaxa and addresses frequently asked questions. It is organized to help mirror how a new user might approach EcoTaxa for the first time.
Related Resources:
The EcoTaxa reference project featured in this webinar has grown and been made publicly available: Getting Started with EcoTaxa for FlowCam Users: Casco Bay, FlowCam 8000 (10X)
EcoTaxa Guide (Coming Soon): Our team is working on a complementary PDF guide that covers everything in the webinar...and more. Keep an eye on our newsletter for an announcement when it’s ready!
4. Resources from PIQv
The PIQv team in Villefranche also has resources available on their website. The website includes a video overview that’s especially helpful for new users, as well as instrument manuals and EcoTaxa manuals used by the PIQv team. Their website also has all the latest information on how to prepare data using raw FlowCam images via Zooprocess. More information about PIQv is available on their homepage.