IFCB-sync

IFCB-sync allows Imaging FlowCytobot (IFCB) operator groups to share their data through an IFCB dashboard hosted at the Woods Hole Oceanographic Institution (https://habon-ifcb.whoi.edu). Depending on how it's invoked, the program either performs a one-time file synchronization or continuosly monitors a specified data directory, uploading any new files created within the directory to <habon-ifcb.whoi.edu> via a cloud-based data pipeline.

The app is tightly integrated with a Teams-enabled instance of IFCB dashboard. Operator groups have full control over how data are shared and organized. They can also update metadata associated with individual samples. Lastly, IFCB-sync automates the generation of commonly used IFCB data products (blobs, features, and machine-based taxonomic classification).

flowchart TD
    A[IFCB Sensor or data server] --> B[ifcb-sync]
    B --> C[Cloud-mediated data transfer]
    C --> D[File integrity verification]
    D --> E[Automated image accession]
    E --> H[HABON IFCB Dashboard<br/>Teams-enabled]
    E --> F[Image feature extraction<br/>ifcb-analysis v4]
    E -.-> G[Taxonomic Classification<br/>in development]
    F --> H[HABON IFCB Dashboard<br/>Teams-enabled]
    G -.-> H
    H --> I[Web interface]
    H --> J[URL API]
    J --> K[Downstream analysis and visualization]

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Features

• Continuous synchronization of IFCB data directories for near real-time sharing
• One-time synchronization for upload of previously acquired datasets
• Supports Linux, MacOS, and Windows
• Integrated with Teams version of IFCB Dashboard so that external operator teams can manage dataset organization and metadata independently

Quick Start

1. Request an account for access to the HABON-IFCB Dashboard
2. Install IFCB Sync
3. Create a dataset through the HABON-IFCB Dashboard
4. Start synchronization

Documentation

• Concepts – Overview of Teams, Datasets, Bins, and IFCB Dashboard.
• Installation – Install IFCB Sync and configure credentials.
• Command Reference – start, stop, sync, list, and status.
• Dashboard Administration – Create datasets, manage bins, and edit metadata.
• Accessing Dashboard Data – Retrieve metadata, classifier outputs, images, and other products through the URL API.