Herbarium Spectroscopy with MicroNIR

Theory and practice

Introduction

Welcome!😊

This course was designed to train staff and fellows in the use of the portable MicroNIR 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 an application protocol within the SpectraPop Project.

Course details

Where: INPA Herbarium (1st floor, IFN Room), Av. André Araújo, 2.936 - 69067-375 - Petrópolis, Manaus, Amazonas, Brazil.

Date: April 2–4, 2025.

Target audience: Staff and fellows involved in the herbarium workflow who are interested in using portable spectroscopy for scientific research.

Number of places: 13 (previously selected participants).

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

Format: Hybrid, with virtual theoretical classes and in-person practical classes. Four laptops will be available for the practical classes, and the activities will be carried out in four groups.

Material: Slides, scripts and data obtained during the course will be made available directly to the students or via GitHub.

Important notes:

External participants must present a photo ID (e.g., national ID card) and inform staff at any INPA gate that they are taking part in a training at the INPA Herbarium.
For the theoretical classes, participants may attend from home or use INPA’s facilities. If the latter, please let us know in advance.
At the end of the course, each participant must fill in an evaluation form to assess the training and to give suggestions for improving the MicroNIR usage protocol, which will later be made available to the entire interested community.

Schedule

Overview

The workshop activities will take place over three consecutive days, from Wednesday to Friday.

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 (Wednesday)

Morning (Flávia)

Theoretical fundamentals of NIR spectroscopy and its applications

Link to join the class: https://meet.jit.si/Spectrapop

Link to the attendance list: https://forms.gle/PTZiQRaphvAgcDwu7

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

Afternoon (Caroline)

Presentation of the NIR-S-G1 device (MicroNIR, InnoSpectra Corp.) and accessories
Setting up the ISC-NIRScan GUI app (laptop and smartphone)
Calibration, spectral data collection and the care needed when acquiring spectra
Understanding the output files

Link to the attendance list: https://forms.gle/7Y52iFG1BNhstmey6

Day 2 (Thursday)

Morning (Caroline)

Practical exercise in acquiring spectral readings - Example with some of the CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) species listed below:

Id	Family	Species
1	Bignoniaceae	*Handroanthus barbatus*
2	Bignoniaceae	H. capitatus
3	Bignoniaceae	*H. impetiginosus*
4	Bignoniaceae	*H. incanus*
5	Bignoniaceae	*H. ochraceus*
6	Bignoniaceae	H. serratifolius
7	Bignoniaceae	Tabebuia aurea
8	Bignoniaceae	T. insignis
9	Meliaceae	Cedrela odorata
10	Fabaceae	Dipteryx magnifica
11	Fabaceae	D. odorata
12	Fabaceae	D. polyphylla
13	Fabaceae	D. punctata

Link to the attendance list: https://forms.gle/ucjn7CXmNSVrbKdH7

Afternoon (Caroline)

Installing the required libraries
How to import spectral readings into R
How to visualize spectra and assess the quality of spectral data
How to prepare datasets for analysis

Link to the attendance list: https://forms.gle/WnXsJYpzR1aw5kxT8

Day 3 (Friday)

Morning (Flávia)

Theoretical fundamentals of NIR spectroscopy and its applications

Link to join the class: https://meet.jit.si/Spectrapop

Link to the attendance list: https://forms.gle/j6JUzh1RKtncAZT67

Afternoon (Caroline)

Discriminant analysis (LDA) with Leave-One-Out (LOO) cross-validation
Basic model evaluation (accuracy and confusion matrix)
Fill in the course evaluation form

Link to the attendance list: https://forms.gle/BtVwHsepLdAKL55R7

Link to the feedback form: https://forms.gle/jFX8RhJp2MVVybRa9

Organizing and training team

Prof. Dr. Flávia Durgante (SpectraPop Project Coordinator), KIT/MAUA/INPA

Dr. Caroline Vasconcelos (SpectraPop Project fellow, AT/III), INPA

Prof. Dr. Michael Hopkins (Collaborator), INPA Herbarium Curation

Funding

This course is part of the Project “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), and supported by the INPA Herbarium through the MCTI/FINEP/FNDCT Public Call No. 02/2016 – National Multi-User Centers.

Introduction

Course details

Schedule

Overview

Timeline

Day 1 (Wednesday)

Morning (Flávia)

Afternoon (Caroline)

Day 2 (Thursday)

Morning (Caroline)

Afternoon (Caroline)

Day 3 (Friday)

Morning (Flávia)

Afternoon (Caroline)

Organizing and training team

Funding

Participants