Microdialysis vs Fiber Photometry for Neurotransmitters

Microdialysis vs Fiber Photometry for Neurotransmitters

Microdialysis and Fiber Photometry are both powerful techniques for monitoring the concentrations
of neurotransmitters in vivo, but each technique has very different advantages. Amuza is the only company that provides both types of equipment to the neuroscience community, putting us in a unique position to help you determine when microdialysis or fiber photometry would be the best choice.

Microdialysis Fiber Photometry
Best for
  • Monitoring long-lasting changes
  • Absolute concentrations
  • Many analytes
  • Sub nanomolar analytes
  • Monitoring fast changes
  • Relative concentrations
  • One or two analytes
  • Targeting cell subtypes
Sensitivity Picomolar Nanomolar
Multiple analytes Many analytes can be measured in each sample with the little added difficulty Data processing and experimental protocol are both more difficult
Types of analytes Most types of molecules. Limited by available fluorescent sensors
Type of measurement Absolute concentration or % change relative to baseline % Change relative to baseline
Data analysis Relatively simple Often quite complex
Sampling period ~30 seconds to hours Milliseconds
Sampling duration Days Days, but difficult to monitor slow changes
Targeting Brain region/structure The brain region, specific projection, cellular subtype, axon vs cell body
Animal movement Tether required Tether or wireless headstage

Multiple analytes

It is routine to measure many different neurotransmitters or amino acids in each microdialysis sample using HPLC chromatography and electrochemical detection. Samples can also be split and stored before analysis so that additional analytes can be added to the protocol at a later date. Commercially available assays also allow panels of multiple peptides and proteins to be measured in each sample.

Measuring multiple analytes simultaneously using fiber photometry is possible, but it requires expressing multiple fluorescent sensors at the target and the data analysis also becomes much more complex

Types of analytes

Microdialysis is extremely flexible and has been used to measure many types of analytes including amino acids, proteins, peptides, neurotransmitters, sugars, and more. If you can assay for it, you can probably sample for it using microdialysis.

Fiber photometry can now measure most of the principal neurotransmitters but is limited by the fluorescent sensors available. The number of sensors is increasing rapidly, but the options are still smaller than those available to microdialysis users.

Type of measurement

Microdialysis allows the monitoring of absolute concentrations or concentrations relative to basal levels in every sample.

Fiber photometry data yields a change in fluorescence data (∆F/F0). This correlates with changes in the concentration of the analyte relative to baseline but typically isn’t used to determine absolute concentrations.

Data Analysis

HPLC software packages already include all of the functions required to automate the processing of microdialysis data, allowing the monitoring of many analytes simultaneously over time. The analysis can be easily taught to new users. In contrast, fiber photometry data processing is still usually a complex operation, with most labs using multiple software packages and writing their own scripts to deconvolve and analyze multiple streams of data. (TeleFipho photometry data only uses fluorescence data from one wavelength, and is easier to process)

Sampling Period and Duration

While sample times can be as short as 30 seconds, microdialysis excels in measuring long-lasting changes in extracellular concentrations, and for determining absolute concentrations for baseline levels. It is quite routine to continuously sample for many hours or even days during a microdialysis experiment. Furthermore, the microdialysis probe can be removed and replaced with a dummy probe for days or weeks between sampling sessions.

Fiber photometry is at the opposite extreme: fluorescence is measured every 1 to 10 ms, allowing it to record events lasting less than a second. But drift, noise, and photobleaching during fiber photometry experiments complicate observation of slow changes over time.


Both microdialysis and fiber photometry are used to target a discrete region or structure within the brain. Fiber photometry also allows retrograde or anterograde targeting, so that only specific projections are monitored. Viral vectors that only express the sensor in a specific cellular subtype or target either the axon or cell body can further narrow the scope of the events recorded.

Animal movement

Microdialysis and fiber photometry both typically require a tether during the experiment. TeleFipho is the exception and uses a wireless rechargeable headstage to gather and transmit fiber photometry data.

Do you have a question about microdialysis or fiber photometry?

GECIs and GEFIs: A Guide for Choosing Fluorescent biosensors for fiber photometry

GECIs and GEFIs: A Guide for Choosing Fluorescent biosensors for fiber photometry

Updated on September 16, 2020

Fiber Photometry is a rapidly advancing field, with biosensors for more analytes and with better sensitivity being announced almost every month. We would like to share information about sensors that should be compatible with fiber photometry when using excitation with blue (~480 nm) light and measuring green (~525 nm) fluorescence. This is the most commonly used wavelength pair and is the one offered with TeleFipho wireless fiber photometry.

We will update this guide as more information becomes available.

Overview of Fluorescent indicators: Structure and considerations for use.

Genetically encoded fluorescent indicators (GEFIs) are used in conjunction with fiber photometry to report on changes in concentrations of molecules in vivo in real-time.

Most fluorescent biosensors consist of a fluorescent protein yoked to an analyte binding protein, constructed so that binding of the analyte causes a dramatic increase in fluorescence.

Akerboom, Rivera, Guilbe, Malavé, Hernandez, Tian, Hires, Marvin, Looger, Schreiter ER / CC BY (https://creativecommons.org/licenses/by/3.0)

When used with fiber photometry in behaving animals, the sensors are usually introduced by injecting viral expression vectors. The virus is used to both express the sensor and to control its location: targeting sequences allow the researcher to choose a specific cellular subtype, and even the cellular localization, such as axon or soma, where the sensor will be expressed. Anterograde and retrograde localization can also be used to target only a specific projection or circuit in a target region. Transgenic animals are also available for expressing some GEFIs.

Binding kinetics help determine the range of concentrations the sensor will respond to, as well as its ability to report fast events. A sensor with high affinity (low Kd) and a long dissociation time can measure very low concentrations of a molecule, but this happens at the expense of being able to resolve more frequent events and a narrower useful range of concentrations. Fast dissociation improves time resolution, but sensitivity usually suffers.

The brightness of the sensor, partially expressed as the ratio of the increase in fluorescence when bound to the analyte compared to baseline (∆F/F or ∆F/F0 ), is the other major factor to consider. Brighter sensors can generate a useful signal when expressed at lower levels or when used with less illumination when compared to less bright sensors.

Most biosensors are already available from AddGene: some as plasmids, others as aliquots of ready to use viral vectors. The newest biosensors listed here can be sourced directly from the laboratories which invented them. We included the best source we could find, as well as the original publication describing the sensor in the table below.


Calcium Sensors Affinity (Kd or EC50) dissociation
Kinetics (Mean life,
∆F/F0 (% increase) Source for vector or plasmid Reference
GCaMP6s 147 nM 1796 ms 1680
Chen, 2013
GCaMP6f 375 nM 400 ms 1314
Chen, 2013
jGCaMP7s 68 nM 1260 ms
Dana, 2019
jGCaMP7f 270 ms
Dana, 2019
Yang, 2018
The GCaMP6 series of genetically encoded Ca2+ indicators (GECIs) are the most popular tools for examining action potentials and have been used extensively with TeleFipho photometry. GCaMP6f is optimized for fast decay kinetics, necessary for monitoring very fast events, while GCaMP6s has higher sensitivity and slower decay kinetics. If you are starting a new project consider the latest generation – jGCaMP7 – which offers higher sensitivity and a larger range of kinetics.

jGCaMP7 is the latest generation of GCaMP sensors, introduced in 2019 as a collaborative effort between Loren Looger at Janelia as well as other research institutes. The jGCaMP7 GECIs have several-fold higher ∆F/F0 and a wider range of kinetics when compared to the earlier GCaMP6 sensors. Some GCaMP7 variants that will be of interest to fiber photometry users include jGCaMP7s (highest sensitivity, but slower kinetics), and jGCaMP7f which has the fastest kinetics. We hope to have calcium data generated using jGCaMP7s and TeleFipho wireless fiber photometry soon.

GCaMP-X The calmodulin GCaMP based calcium sensors have been shown to cause side effects during some in-vivo uses, such as interference with the function of L-type calcium channels, nuclear accumulation, and cytotoxicity. These issues are largely addressed by changes to the design of GCaMP-X.


Dopamine is rapidly becoming the second most common target for imaging and photometry in neuroscience thanks to two sensors introduced in 2018, dLight and GRABDA. The intensity of illumination used with dLight and GRABDA is typically 20 – 30 μW, the same range as is used with GCaMP6.

Dopamine sensors Affinity (Kd or EC50) dissociation
Kinetics (residence time, τ = 1/Koff)
∆F/F0 (% increase) Source for vector or plasmid Reference
dLight1.1 330 nM NA 230
Patriarchi, 2018
dLight1.2 770 nM 90 ms 340
Patriarchy, 2018
GRABDA1m 130 nM 700 ms 90
Sun, 2018
GRABDA2m 90 nM NA 340
Yulong Li Lab
Sun, 2020
GRABDA1h 10 nm 2500 ms 90
Sun, 2018
GRABDA2h 7 nM NA 280
Yulong Li Lab
Sun, 2020

dLight1.1 and dLight1.2, developed by the Tian lab, have both been used extensively with fiber photometry, with settings similar to those used for GCaMP6.


GRABDA (GPCR-Activation Based DA) was first introduced by Yulong Li’s lab in 2018 and has just been updated to increase Δf/f and increase the range of kinetics. The new versions are DA2H (high affinity) and DA2M (medium affinity). Both GRABDA2m and GRABDA2H have already been used with fiber photometry, but so far results have only been communicated via preprints.

Norepinephrine and Serotonin

More from the Yulong Li lab, though as of yet their characterization is only available through preprints. GRABNE1m and GRAB5-HT1.0 have both already been used to measure norepinephrine and serotonin via fiber photometry in mice.

Sensors Analyte Affinity
(Kd or EC50)
dissociation Kinetics
( τ = 1/Koff))
∆F/F0 (% increase) Source for vector or plasmid Reference
GRABNE1h Norepinephrine 83 nM 2000 ms 130
Yulong Li Lab
Feng, 2019
GRABNE1m Norepinephrine 930 nM 750 ms 250
Yulong Li Lab
Feng, 2019
GRAB-5HT1.0 Serotonin 22 nM 3.1 s 280
Yulong Li Lab
Wan, 2020
iSeroSnFr Serotonin
Tian Lab
Unger, 2020

Biosensors for endocannabinoids (GRABeCB), ATP, cholecystokinin (CCK), vasoactive intestinal peptide (VIP), somatostatin (SST), vasopressin/oxytocin, ghrelin, and orexin were also announced by the Li lab at Neuroscience 2019, and are still being validated. The best way to keep up with the Li lab may be checking #GRABSensors on Twitter!
More information on iSeroSnFr from the Tian lab should be available soon.


GABA Sensors Affinity (Kd or EC50 dissociation
(τ = 1/Koff)
∆F/F0 (% increase) Source Reference
iGABASnFR 9 μM 250
Marvin, 2019


There are two main sensor types available for monitoring glutamate: iGluSnFR and iGlu. The original iGluSnFR has slower kinetics, while iGluf (fast) and iGluu (ultrafast) are much faster. The new SF-iGluSnFR variants offer higher brightness and a range of different kinetics compared to the original.

Glutamate Sensors Affinity (Kd or EC50 dissociation
(τ = 1/Koff)
>∆F/F0 (% increase) Source Reference
iGluSnFR 4.9 μM 92 ms 100
Marvin, 2018
iGluf 137 μM 2.1 ms
Helassa, 2018
iGluu 600 μM 0.7
Helassa, 2018


Acetylcholine Sensors Affinity (Kd or EC50 dissociation
(τ = 1/Koff)
∆F/F0 (% increase) Source Reference
iACHSnFR 1.3 µM 1200
Borden, 2020
ACh3.0 2 μM 3.7s
Yulong Li Lab
Jing, 2019
Yulong Li Lab

iACHSnFR is one of the most recent GEFIs created by the Loren Looger lab at Janelia, along with collaborators.

While the initial version of the GRAB type acetylcholine indicator (GACH) was not sensitive enough for measuring physiological levels of ACh using fiber photometry (personal communication), the version described in a preprint from Dec. 2019 (ACh3.0) has been used successfully with fiber photometry. The Li lab is also supplying researchers with an even newer version, ACh4.3.

Other Analytes

Sensors Analyte Affinity (Kd or EC50 dissociation
(τ = 1/Koff)
∆F/F0 (% increase) Source for vector or plasmid Reference
GRABAdo Adenosine 60 nM 63 ms 120
Yulong Li Lab
Peng, 2020

Peng et al. monitored adenosine in the mouse basal forebrain using fiber photometry and  GRABAdo, also called Ado1.0

Please let us know if you have any corrections or additions for this list!

TeleFipho is the world’s first commercially available wireless fiber photometry system. It is a turnkey system tested in both mice and rats. If you would like to know more:

Both TeleFipho and the Teleopto Wireless Optogenetics system now accept standard Ø2.5 mm FC cannulae, commonly used with patchcord-connected optogenetics and fiber photometry systems allowing you to use the same implanted fiber-optic cannula with either system.
Telefipho Wireless Fiber Photometry

Telefipho Wireless Fiber Photometry

We would like to tell you about TeleFipho, Amuza’s new wireless fiber photometry system. It’s our newest way to track calcium and neurotransmitters, and it works in real-time in freely moving animals. It’s easy to use, easy to process your data, and it’s ready to go right out of the box.

Fiber photometry is one of the newest tools available to neuroscientists who wish to correlate behavior with neural activity. It’s a powerful, ultra-fast technique used to measure calcium, neurotransmitters and other molecules in vivo in real-time. But until now the technique has required a connection – a fiber optic cable connecting the research animal to the rest of the optical hardware outside of the cage. This cable limits animals’ freedom of movement and social interactions. It is also fragile and can make your data noisier. This, in turn, can limit the design of your experiments.

Fiber Photometry Schematic

Telefipho Schematic

With Telefipho all of the optical hardware – light source, optical filters, and photodetector – are combined in a small headstage. The rechargeable headstage communicates by radio with a base station. Your animals can move through tunnels and doorways and interact freely during experiments. Telefipho can also improve video tracking: tracking software often confuses a swaying cable with a mouse that is still moving. This can complicate the scoring of freezing behavior during fear conditioning.

The headstage mounts directly on an FC size fiber optic cannula without any intervening cables or interconnects. This maximizes light transmission and minimizes noise and artifacts. This headstage weighs just 3 grams and has been tested with both mice and rats.

To use the system, an optical fiber is implanted with the tip placed at the brain region of interest. Blue light from an LED in the headstage is sent through the fiber to excite the fluorescent sensors expressed in the target region. The sensor molecules fluoresce in proportion to the concentration of the analytes, and some of the fluorescent light travels back through the fiber to be measured by a photodetector. A fluorescence filter cube, combining bandpass filters for excitation, a bandpass filter for emission, and dichroic mirrors are used to remove extraneous wavelengths and separate the light paths. The headstage transmits the data to the base station and then to your computer.

Since only a single narrow fiber is implanted inside the skull, the technique is much less invasive than imaging, especially for targets deep inside the brain.
The fluorescent signal is recorded and allows tracking of changes in analyte levels on a subsecond time scale.

TeleFipho data is also easy to work with. Removing the cable means removing the motion artifacts caused by rotary joints and long flexible waveguides, so you won’t have to process your data to correct for them.

TeleFipho software provides a real-time view of the data, allowing you to quickly optimize light levels and detection sensitivity. You can manually add timestamps and notes to the data, or you can connect your behavioral equipments’ outputs to TeleFipho and automatically align behavioral events with the fluorescence data.

You can also send the signal to your own recording equipment and process the data using your own software.

With the ever-increasing number of genetically encoded fluorescent indicators for molecules beyond calcium, such as dopamine, glutamate, acetylcholine, norepinephrine, endocannabinoids, and even cyclic monophosphates, fiber photometry is certain to become a versatile tool in your lab. This is doubly true since the vectors used to express the sensors are becoming increasingly precise at targeting specific cell types and circuits so that results are increasingly specific with less interference from off-target cells and molecules.

If you would like to learn more about TeleFipho fiber photometry, please contact Amuza.


Wireless Fiber Photometry: Measuring Neurochemicals In Vivo in Real Time

Wireless Fiber Photometry: Measuring Neurochemicals In Vivo in Real Time

Amuza and Teleopto launch the first commercial wireless fiber photometry system at Neuroscience 2019

Our wireless optogenetic users have frequently asked us if we could provide wireless photometry – we are happy to announce that now we can!

TeleFipho wireless headstages allow your freely behaving animals to move with true freedom, enabling novel experimental approaches with fiber photometry. The 3 gram headstages are optimized for GCaMP and other GFP based indicators.

TeleFipho includes all of the components required for fiber photometry – light source, filter cube, photodetector, and wireless transmission hardware – in a 3 gram headstage.

What is Fiber Photometry?

Fiber Photometry is a powerful technique for measuring rapid changes in neuromodulators in vivo via fluorescence. It is most commonly used  to measure fast (subsecond) changes in concentrations of calcium in freely behaving animals, but it is now also capable of being used to monitor neurotransmitters and other molecules.To use fiber photometry, genetically encoded fluorescent indicators are first expressed at the location of interest. When excited by light of the right wavelength, these proteins fluoresce – but only while they are bound to their target analyte. As local concentrations of the analyte rise and fall, the fluorescence intensity rises and falls in response. Genetically encoded calcium indicators (GECIs), such as GcAMP have been the mainstay of fiber photometry and also for calcium imaging, a closely related technique. Recently dopamine indicators (Dlight1, GRABDA) and norepinephrine indicators (GRABNE) have been introduced, and more neurochemical sensors are in development. 

To capture this signal  in vivo, an optical fiber is implanted at the target region in the animal. The other end of the fiber is attached to the photometry hardware. First an LED or laser light source passes light through the fiber to excite the indicator proteins in the target region. The resulting fluorescent light then travels back through the fiber to a photodetector, creating a record of the changing concentrations of the analyte. Careful filtering and splitting of the light traveling through the fiber optic is required to separate the light used for excitation from the fluorescence being sent to the photodetector. 

Why use Fiber Photometry?

The most frequent use is to measure changes in calcium levels at synapses as a proxy for changes in neural activity, helping researchers discern the links between behavior states and the firing patterns of neurons. But the same technique is also used to monitor the activity of GPCRs and ion channel drug targets. 

When used with freely moving animals, fiber optic tethers can be problematic. The cable can prevent animals from using exercise wheels or shelters or get tangled in complicated environments, limiting behavioral testing. Cables can also cause artifacts when used with video tracking software. For example, the cable often continues to sway after the animal has stopped moving, making it difficult to recognize freezing behavior during fear conditioning studies. Placing all of the necessary components for fiber photometry in a small lightweight headstage ends these problems.

TeleFipho has been tested with both mice and rats. The data above shows stress induced (tail pinch) changes in GCaMP signals from hypothalamic orexin neurons in mice. GCaMP is a genetically encoded calcium indicator often used to monitor calcium dynamics. Data is Courtesy of Dr. Daisuke Ono in the Akihiro Yamanaka Lab, Nagoya University.

Shrinking the components for fiber photometry has an added bonus: it also allows us to shrink the price. Telefipho starts at roughly half of the cost of other commercial fiber photometry systems.

Please stop by our booth during SfN 2019 to ask for a demonstration and visit our product page for more information.