NCZarr Viewer

Exploring and Subsetting Zarr & NetCDF Data
2 Sept 2025
Samuel Fooks — VLIZ
Funded by the European Union

NCZarr Viewer

  • 📊 Load and explore Analysis Ready Cloud Optimized(ARCO) NetCDF and Zarr datasets
  • 🔍 Browse variables and dimensions through a simple interface
  • ✂️ Subset data by time, space, and other dimensions visually
  • 📈 Visualize results with interactive plots
  • 🐳 Containerized for easy deployment and sharing
  • In EDITO Datalab!
Funded by the European Union

🛠️ Technology Stack

  • Frontend: Dash + Bootstrap Components
  • Data Processing: Xarray + NumPy
  • File Formats: NetCDF4, Zarr
  • Visualization: Plotly, Matplotlib, Cartopy
Funded by the European Union

🚀 Quick Start

On EDITO

DOCKER

docker run -p 8050:8050 samfooks/nczarr-viewer:latest

LOCAL DEV

git clone https://github.com/EDITO-Infra/nczarr-viewer
cd nczarr-viewer
pip install -r requirements.txt
python run.py

Access at: http://localhost:8050
💡 Tip: Think of this as "R Shiny for NetCDF data" - but already built for you!

Funded by the European Union

📁 Supported Data Sources

  • ARCO data on EDITO: Analysis Ready Cloud Optimized datasets from the EDITO STAC
  • Personal Cloud Storage: Minio storage on EDITO
  • Local Files: NetCDF, Zarr
Funded by the European Union

🔍 Core Features

Data Exploration

  • Variable Browser: See all variables, dimensions, and metadata
  • Dimension Handling: Time, depth, latitude, longitude
  • Data Subsetting: Interactive selection of regions and time periods

Visualization

  • Interactive Maps: Cartopy-based geographic plots
  • Time Series: Plotly charts for temporal data
  • Statistical Analysis: Basic stats, and summaries
Funded by the European Union

🌊 Marine Data Examples

EDITO STAC

  • Chemistry: Water quality parameters
  • Geology: Seafloor characteristics
  • Biodiversity: Species distribution data

Copernicus Marine

  • Access: CMEMS credentials integration (you will need an account)
  • Multiple Formats: NetCDF, Zarr (and others in future)
  • Real-time Data: Latest ocean observations
Funded by the European Union

🔍 Subsetting ARCO Data: Core Concepts

Multidimensional Data Structure

┌─────────────────────────────────────────────────────────┐
│                    ARCO Dataset                        │
├─────────────────────────────────────────────────────────┤
│  Variables: temperature, salinity, oxygen, etc.        │
│  Dimensions: time, depth, latitude, longitude          │
│  Shape: (time: 365, depth: 50, lat: 1800, lon: 3600) │
└─────────────────────────────────────────────────────────┘

Subsetting Operations

  • Variable: Pick specific parameters
  • Temporal: Select specific dates
  • Spatial: Choose latitude/longitude boundaries
  • Depth: Select depth(elevation)
Funded by the European Union

🎯 Subsetting in Practice

Example: Extract Surface Temperature for North Sea

import xarray as xr

# Load ARCO dataset
ds = xr.open_zarr("s3://arco-data/ocean-temp.zarr")

# Variable: surface temperature
temp_surface = ds['temperature'].sel(depth=0)

# Temporal: August 30
august30_data = temp_surface.sel(
    time='2025-08-30'
)
# Spatial bounds: North Sea region
north_sea = august30_data.sel(
    latitude=slice(51.0, 61.0),    # 51°N to 61°N
    longitude=slice(-5.0, 15.0)    # 5°W to 15°E
)
Funded by the European Union

Visual Representation

┌─────────────────────────────────────────────────────────┐
│  Original: 365×50×1800×3600                           │
│  ↓ Variable selection                                  │
│  Surface: 365×1×1800×3600                             │
│  ↓ Temporal subset                                     │
│  August 30, 2025: 1×1×1800×3600                       │
│  ↓ Spatial subset                                      │
│  North Sea region: 1×1×100×200                        │
└─────────────────────────────────────────────────────────┘
Funded by the European Union

🌊 Use the NCZarr Viewer locally or on EDITO

Video link

Funded by the European Union
Explore a NetCDF from your Minio bucket on EDITO

Video link

Funded by the European Union

🌊 Live Demo Time!

Video link

Funded by the European Union

🔮 Future Developments

  • More Interactive Visualization: More interactive global maps and plots
  • Advanced Analytics: Statistical modeling tools/plugins
  • New ARCO Data types: Parquet, Geoparquet
  • Collaboration: Multi-user editing and sharing
Funded by the European Union

🌊 Thank You!

Samuel Fooks - samuel.fooks@vliz.be
GitHub: https://github.com/EDITO-Infra/nczarr-viewer
DOC Pages https://edito-infra.github.io/nczarr-viewer
Docker Hub: samfooks/nczarr-viewer:latest

Questions?

Funded by the European Union