BioSCape Data Workshop

BioSCape, the Biodiversity Survey of the Cape, is NASA’s first biodiversity-focused airborne and field campaign that was conducted in South Africa in 2023. BioSCape’s primary objective is to study the structure, function, and composition of the region’s ecosystems, and how and why they are changing.

BioSCape’s airborne dataset is unprecedented, with AVIRIS-NG, PRISM, and HyTES imaging spectrometers capturing spectral data across the UV, visible and infrared at high resolution and LVIS acquiring coincident full-waveform lidar. BioSCape’s field dataset is equally impressive, with 18 PI-led projects collecting data ranging from the diversity and phylogeny of plants, kelp and phytoplankton, eDNA, landscape acoustics, plant traits, blue carbon accounting, and more

This workshop will equip participants with the skills to find, subset, and visualize the various BioSCape field and airborne (imaging spectroscopy and full-waveform lidar) data sets. Participants will learn data skills through worked examples in terrestrial and aquatic ecosystems, including: wrangling lidar data, performing band math calculations, calculating spectral diversity metrics, machine learning and image classification, and mapping functional traits using partial least squares regression. The workshop format is a mix of expert talks and interactive coding notebooks and will be run through the BioSCape Cloud computing environment.

Date: October 9 - 11, 2024 Cape Town, South Africa

Host: NASA’s Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC), in close collaboration with BioSCape, the South African Environmental Observation Network (SAEON), the University of Wisconsin Madison (Phil Townsend), The Nature Conservancy (Glenn Moncrieff), the University of California Merced (Erin Hestir), the University of Cape Town (Jasper Slingsby), Jet Propulsion Laboratory (Kerry Cawse-Nicholson), and UNESCO.

Instructors:

• In-person contributors: Anabelle Cardoso, Erin Hestir, Phil Townsend, Henry Frye, Glenn Moncrieff, Jasper Slingsby, Michele Thornton, Rupesh Shrestha

• Virtual contributors: Kerry Cawse-Nicholson, Nico Stork, Kyle Kovach

Audience: This training is primarily intended for government natural resource management agency representatives and field technicians in South Africa, as well as local academics and students, especially those connected to the BioSCape Team.

Presentations

• Workshop Agenda

Presentations - Day 1

• Welcome

• BioSCape Overview

• NASA Earthdata

• Earthdata Search

• The BioSCape Cloud

• JupyterHub Basics

• BioSCape Airborne Data

• BioSCape Field Data

• LVIS and GEDI for post-fire vegetation growth

Presentations - Day 2

• HyTES and ECOSTRESS data

• PRISM, PACE, and ECOSTRESS for aquatic biodiversity

• AVIRIS-NG for spectral diversity

• AVIRIS-NG for mapping alien trees

Presentation - Day 3

• AVIRIS-NG and field data to explore functional traits

Tutorials

Prerequisites

• Earthdata Login
• Compute Environment

Tutorials - Day 1

• 1. Jupyter Notebook Basics
• 2. BioSCape SMCE Basics
• 3. EMIT Files Concurrent with BioSCape
• 4. Exploring, Visualizing, and Plotting BioSCape Field and AVIRIS-NG Data
• 5. Extract, Export to CSV, and Visualize Vegetation Plot Reflectance from AVIRIS-NG
• 6. Exploring and Visualizing BioSCape PRISM Data
• 7. Exploring and Visualizing BioSCape LVIS Data

Tutorials - Day 2

• 1. Computing and Visualizing Spectral Diversity
• 2. Calculate Turbidity from PRISM data
• 3. Exploring an Algal Bloom with Band Math
• 4. Exploring EMIT data and inspecting spectra for alien species
• 5. ECOSTRESS Files Concurrent with BioSCape
• 6. Accessing and Visualizing HyTES data
• 7. Working with multidimensional spatial data in Python
• 8. Mapping invasive species using supervised machine learning and AVIRIS-NG

Tutorials - Day 3

• 1. Townsend Part 1 Tutorial: BioSCape vegetation surveys, community-weighted traits, and AVIRIS-NG
• 2. Townsend Part 2: Plotting the observed vs. predicted
• 3. Part 3 - Foliar Trait Mapping
• 4. Part 3 - Foliar Trait Mapping

Resources

• Other Resources