Herbarium Spectroscopy with portable NIR

Theory and practice

Introduction

Welcome!😊

This course was designed to train students and professionals in the use of the portable spectrometer, covering everything from the initial setup of the equipment to the analysis of spectral data.

Over three days of theoretical and practical activities, participants will explore the fundamentals of near-infrared (NIR) spectroscopy and its application to plant identification.

In addition, the course seeks to identify practical challenges in the use of the equipment, contributing to the development of a standardized application protocol within the SpectraPop Project.

Course details

Where: Auditorium, Mamirauá Institute for Sustainable Development, Estrada do Bexiga, 2584 - 69553-225 - Fonte Boa, Tefé, Amazonas, Brazil.

Date: June 9–11, 2026.

Target audience: Students and professionals involved in the herbarium/reference collection workflow who are interested in using portable spectroscopy for scientific research.

Number of places: 16 (in-person places).

Course load: 18 h (a certificate of participation will be issued).

Format: In-person course, with theoretical classes and practical activities. Four laptops will be available for the practical activities, and participants will be organized into four groups.

Material: The course material will be made available directly to participants or via ⬇️ Download.

Schedule

Overview

The course activities will take place over three consecutive days, from Tuesday to Thursday.

Morning sessions will run from 9:00 am to 12:00 pm (Amazonas standard time).

Afternoon sessions will run from 2:00 pm to 5:00 pm (Amazonas standard time).

Timeline

Day 1 (Tuesday, June 9)

Morning

  • Theoretical fundamentals of NIR spectroscopy and its applications - part I

📚 Complementary material: Video – Tour of the Electromagnetic Spectrum (NASA): https://www.youtube.com/watch?v=2p7FPFvu_j0

Afternoon

  • Presentation of the NIR-S-G1 device (InnoSpectra Corp.) and accessories

  • Setting up the ISC-NIRScan GUI app

  • Introduction to the portable NIR workflow

Day 2 (Wednesday, June 10)

Morning

  • Practical exercise in acquiring spectra and metadata from herbarium specimens

  • The species listed at this link will be tested during the course.

Afternoon

  • Practical exercise in acquiring spectra and metadata from herbarium specimens

Day 3 (Thursday, June 11)

Morning

  • Theoretical fundamentals of NIR spectroscopy and its applications - part II

Afternoon

  • In the R environment:
    • Installing and loading the required libraries
    • Importing spectral data
    • Visualization: assessing spectra quality and PCA
    • Preparing the data for analysis
    • Discriminant analysis (LDA) with Leave-One-Out (LOO) cross-validation
    • Performance evaluation (accuracy and confusion matrix)
    • Interpreting the results
  • Final remarks on the course

Organizing and training team

Prof. Dr. Flávia Durgante (Coordinator of the SpectraPop/HerbSpectra-Amazônia Projects), MAUA/ATTO/INPA

Dr. Samyra Ramos (HerbSpectra-Amazônia Project fellow), MAUA/INPA

MSc Kaio Cunha (HerbSpectra-Amazônia Project fellow), MAUA/INPA

Dr. Kelly Torralvo (SpectraPop Project collaborator), IDSM

Dr. Darlene Gris (SpectraPop Project collaborator), IDSM

Funding

This course is supported by the projects “Amazonian Spectral Herbaria Network: Spectroscopy and artificial intelligence for the automated identification of biodiversity in Amazonian herbaria - HerbSpectra-Amazônia”, funded by the National Council for Scientific and Technological Development (CNPq), Public Call MCTI/CNPq No. 03/2025 - Pró-Amazônia (process no. 385465/2025-4); and “Popularization of the use of the Species Spectral Signature in the identification of trees in Sustainable Forest Management in the Amazon - SPECTRA POP”, funded by the Amazonas State Research Support Foundation (FAPEAM), Call No. 006/2024 - Mulher Faz Ciência (Process No. 01.02.016301.04984/2024-17). The course is also supported by the INPA Herbarium through the MCTI/FINEP/FNDCT Public Call No. 02/2016 – National Multi-User Centers.

Participants

Participants of the 6th SpectraPop Project Course, Mamirauá Institute for Sustainable Development, Tefé, AM. June 2026.

Certificates

To generate your certificate, fill in the form: https://forms.gle/TMPSEC3PMazXsBUs6