In Vivo Calcium Imaging:
The Ultimate Guide

Chapter 1: What is In Vivo Calcium Imaging?

The brain contains over a billion neurons, each with complex networks of connections throughout the brain. Patterns of neural activity are believed to generate specific aspects of behaviour and cognition, but how?

In order to decode patterns of neural activity, neuroscientists need to visualize hundreds of neurons simultaneously—not just an individual neuron—in freely-behaving animals. From a technology standpoint, this is no easy feat.

Current techniques, such as in vivo electrophysiology, can record neural activity with spike-timed precision, but lacks the ability to localize the activity of large populations of individual cells and identify cell types.

Is there a method to visualize neural activity in vivo?

Calcium Imaging

What is In Vivo Calcium Imaging?

Calcium imaging enables neuroscientists to visualize activity in hundreds of individual neurons simultaneously using fluorescent activity sensors. Changes in fluorescence indicate fluctuations in intracellular calcium, which is an indirect indicator of neural activity (1).

The development of genetically encoded calcium indicators (GECIs) has enabled neuroscientists to study specific cell types (e.g. excitatory or inhibitory neurons).

GCaMP, a green fluorescent GECI, is commonly used in calcium imaging experiments since it has been optimized over many generations (currently GCaMP7) for speed, signal-to-noise ratio, expression, and changes in fluorescence (2). The calcium imaging toolbox is constantly growing with the development of new GECIs, such as RCaMP and XCaMP (3,4).

in vivo calcium imaging diagram

Why Use In Vivo Calcium Imaging?

Recently, there has been a surge in the use of calcium imaging to study neural circuits in vivo. This popularization has led to optimized biological methods and better technology, allowing more neuroscientists to adopt the technique.

Aside from popularity, are their other reasons neuroscientists are drawn to calcium imaging?

Calcium imaging provides neuroscientists with the means to study specific populations of cells within or across brain regions in freely-behaving animals. In doing so, neuroscientists can investigate how neural activity may be linked to aspects of behaviour and cognition, effectively linking genetically-identified cells with function.

Behaviour and cognition cannot be characterized by an isolated firing pattern of neurons because they are learned or adapted over time. Calcium imaging can be used to track the activity of neurons over time and investigate how networks grow or change during learning. This is especially important for the longitudinal study of animal models of brain disease. Neuroscientists can begin to understand the development of activity-related changes in these models and assess the long-term effects of pharmacological interventions.

With any new technique, there are associated pitfalls. As we’ve known for years, neural activity is associated with action potentials — changes in voltage across the cell membrane. Calcium imaging measures changes in intra-cellular calcium concentration, providing an indirect indicator of neural activity. Compared to changes in voltage, fluctuations in calcium levels are much slower and may reflect a summation of signals rather than individual spikes (5). That is to say the temporal resolution of calcium imaging may be limited for fast-spiking neurons, such as interneurons.

The gradual development of genetically encoded voltage indicators (GEVIs), designed to detect changes in voltage, are expected to overcome these limitations (6). As with any new technology, widespread application of GEVIs will take time, requiring validation and optimization for use in vivo.

Despite this limitation of calcium imaging, this technique has still greatly advanced our understanding of how neural activity relates to behaviour and cognition.

Visualize and Manipulate Neural Circuits
in Freely-Behaving Animals

Chapter 2: What Do You Need to Perform In Vivo Calcium Imaging?

If someone were to describe in vivo calcium imaging to you, it might sound quite simple.

When you dig deeper, you start to appreciate the complexity associated with the biology and equipment to perform calcium imaging in freely-behaving animals.

You’re probably asking, what are the necessary components to perform in vivo calcium imaging?

Biological Components

Brains don’t naturally express genetically encoded calcium indicators (GECIs), meaning there are biological steps to perform calcium imaging in freely-behaving animals. First, you must express the genetic indicator in the brain; and second, you need to implant an imaging probe to collect fluorescent signals from the brain.

Genetic Sensor Expression

The first and most important step is achieving optimal GECI expression in your animal model.

Mice are the most common animal model used for in vivo calcium imaging due to the advancement of genetic mice models (1); however, calcium imaging has slowly progressed in rats and non-human primates (2,3).

Neuroscientists employ two methods to express GECIs in the brain: viral expression and transgenic mouse models.

Viral expression involves injecting a virus encoding a GECI in the brain. This virus is linked to a gene of interest to target expression in a specific cell-type.

A crucial step associated with viral expression is testing varying dilutions of the virus to obtain optimal expression in the brain (4). Too little expression can lead to no signal, and over-expression can lead to high background fluorescence – or even cell death!

Neuroscientists employ viral expression to regulate GECI expression. This is useful because expression can vary depending on the brain region, cell-type, or virus. In addition, neuroscientists can use viral expression to express GECIs in brain projections to map neural circuits across brain regions.

In comparison to manual viral injections, transgenic mice models are designed to express the GECI throughout the entire brain (5). Depending on the transgenic model, GECI expression can vary from region to region, such that one region may express the GECI more than the other. Neuroscientists examining large cortical areas use these models as they require much more widespread expression, rather than a single region of interest (5).

in vivo calcium imaging viral expression versus transgenic diagram

Imaging Probe Implantation

After successful GECI expression, you need to access the fluorescent signal inside the brain. But how can you see into the brain when it’s covered by both skin and skull?

Generally, this involves surgically implanting an imaging probe into the brain where the GECI is expressed. There are three types of probes (optical cannula, cortical window, GRIN lens) that are used for in vivo calcium imaging. The probe you select is dependent on two factors:

  1. Do you require single-cell resolution imaging?
  2. Will you be imaging in a deep or surface brain region?

Optical cannulas enable light to be delivered and collected from the brain. These probes are used in Fiber Photometry (this will be discussed in the next post) experiments. Due to their design, optical cannulas are only capable of collecting one signal or a population signal—providing little or no spatial resolution to image individual cells. Depending on the length of the optical cannula, they can be used to collect signal in shallow or deep brain regions. Another bonus is optical cannulas are the least invasive surgery because of the compact design, which damages minimal tissue.

In contrast, cortical windows replace a large portion of the skull with a glass window. Neuroscientists employ cortical windows when imaging a large cortical region on the surface of the brain. Cortical windows provide access to the cortex for single-cell resolution recordings.

Lastly, a GRIN lens is a microendoscopic probe that can be implanted in the brain to image deep regions of the brain (up to 8mm) with single-cell resolution. GRIN lens differ in lengths, enabling neuroscientists to image shallow to deep brain regions. To minimize tissue damage, GRIN lenses are typically limited in diameter (0.5mm – 1mm). The GRIN lens diameter restricts the field of view, and thus, imaging with GRIN lenses usually provides a relatively small field of view, especially compared to cortical windows.

in vivo calcium imaging GRIN lens versus cannula

Equipment Components

Now that you have all biological components setup, including optimal GECI expression and imaging probe implantation, you need equipment to record fluorescent signals from the brain of a freely-behaving animal.

The systems currently available for in vivo calcium imaging (which we will discuss in the next post) are comprised of three main components:

    1. Coupling between the imaging probe and imaging device
    2. Light source and filter set
    3. Imaging device
in vivo calcium imaging setup diagram

Coupling Between Imaging Probe and Imaging Device

A fluorescent signal is emitted from the GECI and this is transmitted through the imaging probe. But how can signal be collected?

First, you need a coupling between the imaging probe, light source, and imaging device. This coupling enables illumination of the GECI in the brain through the imaging probe and transmission of the emission signal to the camera. Depending on the calcium imaging system design, a coupling may be achieved via an imaging fiber, or an optical fiber, or the system (such as a miniscope) may be directly mounted onto the head of the animal.

Light Source and Filter Set

Coupling enables you to illuminate and collect fluorescent signals from the brain. GECIs function by generating fluorescence signals, such that they have an excitation and emission spectrum (6). To excite GECIs and collect the emitting signal you require two components: a light source and dichroics/filters.

For excitation of the GECI, LED light sources are commonly selected for in vivo calcium imaging since low optical power is required. However, if a larger region of interest is being illuminated, a higher-power laser may be required. There is a balance between too little and too much power: not getting enough signal and photobleaching your sample.

Importantly, the correct excitation wavelength must be selected. For example, GCaMP excitation is blue (~470nm) and emission is green (~530nm). And this is where the second component is necessary. Dichroics and filters allow proper transmission of the correct excitation wavelength and transmission of the correct emission signal to the imaging device.

Imaging Device

Lastly, you need to collect and analyze fluorescent signals from the brain. This is made possible using an imaging device. Three types of imaging devices are used for in vivo imaging systems: 1) scientific camera, 2) PMT, and 3) photodetector. Which imaging device used is somewhat dependent on the calcium imaging system. If you’re interested in learning more about the differences between imaging devices, this is a helpful article.

Successful in vivo calcium imaging is a balancing act between the biology and equipment. Luckily, both the biology and equipment are constantly being optimized for better performance and ease of use.

Visualize and Manipulate Neural Circuits
in Freely-Behaving Animals

Chapter 3: What Systems are Available for In Vivo Calcium Imaging?

A long-standing objective in neuroscience has been elucidating how in vivo neural activity relates to sensory processing, behaviour, cognition, and cortical processing. Researchers have attempted to understand this relationship by developing a wide-range of all-optical tools for calcium imaging in freely-behaving animals.

The requirements for in vivo calcium imaging vary depending on imaging resolution, animal model, field of view, data collection, and brain region. With a varying degree of requirements, there are different calcium imaging tools available to fully understand the complex connection brain activity and function.

What systems are available for in vivo calcium imaging?

1. Fiber Photometry

Fiber photometry is an in vivo calcium imaging tool that detects average fluorescence intensity changes from population neural activity within a select region of a freely-behaving animal (1). An implanted optical cannula coupled to an optical fiber allows light to be delivered and retrieved from the brain. The acquired signal is then collected by an externally positioned imaging device (photodetector, PMT or camera).

Fiber photometry data acquisition is limited to population level activity with no cellular resolution to visualize individual neurons. The benefit of low cellular resolution is small data files, fast acquisition, and easy data interpretation, unlike other current calcium imaging tools. Thus, fiber photometry provides a low entry barrier for new labs wanting to adopt calcium imaging or perform exploratory research.

The light-weight design and less invasive surgeries make it possible to perform fiber photometry in multiple brain regions simultaneously. Multi-region fiber photometry is performed using a multi-fiber patch cord and imaged onto a camera for data acquisition (2). In comparison, a single region fiber photometry experiment uses a single patch cord is used and signal is captured using a photodetector or PMT.

The light-weight equipment required for fiber photometry helps extend the length of experiments and reduce extraneous factors (e.g. stress) allowing for more natural animal behavior to be observed during experiments. In addition, certain systems can be used with a rotary joint for freely-behaving experiments.

Fiber photometry is a useful tool that can provide us with a better understanding of low level circuitry in the brain. The simplistic design and data output of this tool provides a good starting point for in vivo calcium imaging.

in vivo calcium imaging fiber photometry diagram

2. Miniscope

A miniscope is a miniaturized microscope that mounts on the head of an animal to image neural activity in a freely-behaving animal (3). By coupling a miniscope to an implanted GRIN lens (deep brain) or a cortical window (cortex), you can image individual neurons in a freely-behaving animal. The design of a miniscope is essentially the same as a one-photon microscope, comprised of the appropriate lenses, LED, filters, and camera.

The construction of the miniscope unlocked the ability to image the activity of thousands of individual neurons in freely-behaving animals (3). Freely-behaving capabilities are supported due to the reduced weight of the miniscope that has all the components integrated (~2g) into one system. The minscope provides a field of view that is determined by the size of the implanted GRIN lens (ranging 0.5mm to 1mm diameter) and the selection of GRIN lens will depend on the region of interest.

Recent developments in miniscope technology have enabled researchers to perform dual-colour imaging, wireless calcium imaging, and two-photon calcium imaging in freely-behaving animals (4,5).

The miniaturized design and all components being integrated on the head of the animal allows the animal to behave freely but partially constrains the possible integrated components. These include, low level cameras with low sensitivity and high noise not capable of high cellular imaging resolution, and the number of wavelengths they can illuminate is currently restricted to one or two. Thus, the capabilities of this system and the flexibility for future updates are currently limited.

Miniscopes have advanced our understanding of neural activity. This system can provide further insight into the activity of large neuronal populations for calcium imaging in freely-behaving animals.

in vivo calcium imaging miniscope diagram

3. Optical Fiberscope

The optical fiberscope, such as Mightex’s OASIS implant, is an all-optical system that enables single-cell resolution calcium imaging in freely-behaving animals using an imaging fiber. A removable imaging fiber, coupled with a GRIN lens implanted in the brain or cortical window, provides calcium imaging in the deep brain, cortex, or spinal cord of a freely-behaving animal.

The imaging fiber consists of thousands of individual micro-fibers to image hundreds of individual neurons in freely-behaving animals. An optical fiberscope can also be used to perform population level imaging, identical to fiber photometry. This enables researchers to begin experiments with fiber photometry and later delve deeper using single-cell calcium imaging. Like a miniscope, the optical fiberscope’s field of view is determined by the size of the implanted GRIN lens.

A wide-range of calcium imaging applications can be executed with the optical fiberscope, such as dual-colour imaging and multi-region calcium imaging. The optical fiberscope is the only system that can image multiple brain regions with cellular-resolution — to view individual cells — in a freely-behaving animal.

The flexible imaging fiber and weight of the head-mounted fixture is very low (as little as 0.7g). And, all the electronics are off the head of the animal, compared to a miniscope. Thus, the length of experiments can be extended and extraneous factors (e.g. stress) can be reduced, allowing for more natural animal behavior to be observed. To add to this, the recent implementation of an intricate rotary system enables better freely-behaving experiments.

A vital benefit of the optical fiberscope is the unique flexible design that is scalable and reconfigurable, making it a generic calcium imaging and stimulation platform that can be adapted for different applications, unlike many other single-purpose systems. Two illumination paths allow researchers to attach multiple wide-field and/or targeted light sources with different wavelengths, and to insert different optical filters (e.g. dichroics etc.) suitable for different imaging and/or illumination needs. In addition, this system is compatible with high-quality scientific cameras for capturing better quality images (e.g. with better signal-to-noise ratios and better linearity) for data analysis.

The optical fiberscope is an ideal flexible tool to help understand how single-cell interactions are involved in advanced brain functions, which is not possible with other current technology.

in vivo calcium imaging OASIS Implant diagram

System Comparison Table

technology comparison table
Visualize and Manipulate Neural Circuits
in Freely-Behaving Animals