Leaf spectral signature in herbaria

Theory and practice

Introduction

Welcome!😊

This course was developed within the HerbSpectra-Amazônia Project (Call No. 03/2025 - Pró-Amazônia) to train students and professionals in the use of the portable NIR 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.

Promotional flyer for the course at the Herbarium of the Museu Paraense Emílio Goeldi.

Course details

Where: MG Herbarium, Research Campus - Museu Paraense Emílio Goeldi, Av. Perimetral, 1901 - 66077-830 - Terra Firme, Belém, Pará, Brazil.

Date: May 4–6, 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 streamed live in a virtual environment and practical activities carried out in person. 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 Monday to Wednesday.

Morning sessions will run from 8:30 am to 12:00 pm (local time in Belém).

Afternoon sessions will run from 2:00 pm to 5:00 pm (local time in Belém).

Timeline

Day 1 (Monday, May 4)

Morning (Flávia Durgante)

  • Theoretical fundamentals of NIR spectroscopy and its applications (part I)

▶️ Access to the class: https://meet.jit.si/CursoGoeldi

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

Afternoon (Caroline Vasconcelos, Kaio Cunha and Gabrielly Ribeiro)

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

  • Setting up the ISC-NIRScan GUI app (laptop and smartphone)

  • Introduction to the portable NIR workflow

Day 2 (Tuesday, May 5)

Morning (Caroline Vasconcelos, Kaio Cunha and Gabrielly Ribeiro)

  • Practical exercise in acquiring spectra and metadata from herbarium specimens

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

Afternoon (Caroline Vasconcelos, Kaio Cunha and Gabrielly Ribeiro)

  • Practical exercise in acquiring spectra and metadata from herbarium specimens

Day 3 (Wednesday, May 6)

Morning (Caroline Vasconcelos, Kaio Cunha and Gabrielly Ribeiro)

  • Practical exercise in acquiring spectra and metadata from herbarium specimens

Afternoon (Caroline Vasconcelos, Kaio Cunha, Gabrielly Ribeiro, Flávia Durgante)

  • 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

▶️ Access to the class: https://meet.jit.si/CursoGoeldi

Organizing and training team

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

Dr. Caroline Vasconcelos (HerbSpectra-Amazônia fellow), MAUA/INPA

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

MSc Gabrielly Guabiraba Ribeiro (PhD student at PPGBOT), JBRJ

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); “Building a near-infrared spectral library to reveal new species of Ecclinusa (Sapotaceae, Chrysophylloideae) in South America”, funded by the International Association for Plant Taxonomy (IAPT, 2025 round); 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 5th SpectraPop Project Course and 1st HerbSpectra-Amazônia Project Course, Emílio Goeldi Herbarium, May 2026.

Certificates

To generate your certificate, fill in the form:

🔗 https://forms.gle/3R5HoPVWErxvzQDY8

Certificates can be accessed at the link below. Look for your name in the file list and use the first three digits of your CPF (Brazilian taxpayer ID number) to open the corresponding certificate.

📂 Access certificates