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What is PHOEBE?

PHOEBE (Placing Headgear Optodes Efficiently Before Experiment) is a MATLAB GUI application that measures and displays the optical coupling between fNIRS optodes and the scalp of a subject in real time.

The primary goal of PHOEBE is to help the experimenter optimize signal quality of fNIRS headgear in a time efficient manner. Details on the methods used to quantify the scalp-optode coupling is described in the paper linked at the bottom of this page.

Why using PHOEBE?

Placing all optodes in good contact with the scalp can be a lengthy and often frustrating process, particularly for newer fNIRS investigators with less experience. Usually, experimenters will follow one of these two approaches:

  1. Optodes are placed on the scalp one-by-one after parting hair underneath each optode. When executed carefully, this method yields the best results. However, with recent fNIRS instrumentation encompassing tens of optodes, the preparation of a subject can take a considerable amount of time that may result in subjects to become tired and uncollaborative (particularly pediatric and elderly populations), which may not be acceptable in a clinical setting.

  2. Optodes pre-mounted on headgear are fitted all at once on the subject's scalp, without parting hair. This method is considerably quicker than individual optodes' placement, but often results in several channels containing low optical signal due to light blockage by hair creating poor coupling between optodes and scalp.

Although fNIRS instruments' software may provide a graphical and/or numerical indication of which optical channels (i.e, optode pairings) have poor signal quality, localizing and adjusting individual uncoupled optodes remains a lengthy and difficult process for non-technical personnel.

PHOEBE achieves an optimum trade-off between these approaches by:

  • Determining a quantitative measure of scalp coupling of each individual optode, akin to electrical skin conductance used in EEG, and

  • Displaying the scalp coupling status of all optodes on a head model, so to guide the experimenter to a quick and intuitive adjustment.

#Compatibility with fNIRS instruments

At this time, PHOEBE is compatible with the following instruments:

but it can be expanded to work with any fNIRS instrument that can stream data using LSL (Lab Streaming Layer). We are happy to work with hardware developers interested in interfacing with PHOEBE (see Feature Requests below).

In addition, PHOEBE can be interfaced with Polhemus Patriot for a guided digitization of all optodes and fiducial points in the MNI space.

Table of Contents

Bugs and Feature Requests

To report bugs and suggest additional features, please click on the Issues link on the left sidebar or contact me directly at


PHOEBE has been coded mainly by Luca Pollonini, Ph.D. with contributions by Jonathan Perry, M.S. with the Optical BioImaging Lab at the University of Houston.

We acknowledge the grateful collaborative support of Heather Bortfeld, Ph.D. at University of California, Merced and John Oghalai, M.D. at University of Southern California - Keck School of Medicine, without whom PHOEBE could not have been possible.


If you find PHOEBE helpful for your work, please consider citing this paper:

L. Pollonini, H. Bortfeld, and J. Oghalai, "PHOEBE: a method for real time mapping of optodes-scalp coupling in functional near-infrared spectroscopy," Biomed. Opt. Express 7, 5104-5119 (2016)


PHOEBE is distributed under the Creative Commons BY-NC-SA 4.0 License