Imaging and Optically Manipulating Neuronal Ensembles

Emerging ideas and tools to study the emergent properties of the cortical neural circuits for voluntary motor control in non-human primates

For years, neurophysiological studies of the cerebral cortical mechanisms of voluntary motor control were limited to single-electrode recordings of the activity of one or a few neurons at a time. This approach was supported by the widely accepted belief that single neurons were the fundamental computational units of the brain (the “neuron doctrine”). Experiments were guided by motor-control models that proposed that the motor system attempted to plan and control specific parameters of a desired action, such as the direction, speed or causal forces of a reaching movement in specific coordinate frameworks, and that assumed that the controlled parameters would be expressed in the task-related activity of single neurons. The advent of chronically implanted multi-electrode arrays about 20 years ago permitted the simultaneous recording of the activity of many neurons. This greatly enhanced the ability to study neural control mechanisms at the population level. It has also shifted the focus of the analysis of neural activity from quantifying single-neuron correlates with different movement parameters to probing the structure of multi-neuron activity patterns to identify the emergent computational properties of cortical neural circuits. In particular, recent advances in “dimension reduction” algorithms have attempted to identify specific covariance patterns in multi-neuron activity which are presumed to reflect the underlying computational processes by which neural circuits convert the intention to perform a particular movement into the required causal descending motor commands. These analyses have led to many new perspectives and insights on how cortical motor circuits covertly plan and prepare to initiate a movement without causing muscle contractions, transition from preparation to overt execution of the desired movement, generate muscle-centered motor output commands, and learn new motor skills. Progress is also being made to import optical-imaging and optogenetic toolboxes from rodents to non-human primates to overcome some technical limitations of multi-electrode recording technology.

Two-Color Volumetric Imaging of Neuronal Activity of Cortical Columns

To capture the emergent properties of neural circuits, high-speed volumetric imaging of neural activity at cellular resolution is needed. Here, we introduce wavelength multiplexing to perform fast volumetric two-photon imaging of cortical columns (>2,000 neurons in 10 planes at 10 vol/s), using two different calcium indicators, an electrically tunable lens and a spatial light modulator. We image the activity of neuronal populations from layers 2/3 to 5 of primary visual cortex from awake mice, finding a lack of columnar structures in orientation responses and revealing correlations between layers which differ from trial to trial. We also simultaneously image functional correlations between presynaptic layer 1 axons and postsynaptic layer 2/3 neurons. Wavelength multiplexing enhances high-speed volumetric microscopy and can be combined with other optical multiplexing methods to easily boost imaging throughput.

Synchronized activation of striatal direct and indirect pathways underlies the behavior in unilateral dopamine-depleted mice

For more than three decades it has been known, that striatal neurons become hyperactive after the loss of dopamine input, but the involvement of dopamine (DA) D1‐ or D2‐receptor‐expressing neurons has only been demonstrated indirectly. By recording neuronal activity using fluorescent calcium indicators in D1 or D2 eGFP‐expressing mice, we showed that following dopamine depletion, both types of striatal output neurons are involved in the large increase in neuronal activity generating a characteristic cell assembly of particular neurons that dominate the pattern. When we expressed channelrhodopsin in all the output neurons, light activation in freely moving animals, caused turning like that following dopamine loss. However, if the light stimulation was patterned in pulses the animals circled in the other direction. To explore the neuronal participation during this stimulation we infected normal mice with channelrhodopsin and calcium indicator in striatal output neurons. In slices made from these animals, continuous light stimulation for 15 s induced many cells to be active together and a particular dominant group of neurons, whereas light in patterned pulses activated fewer cells in more variable groups. These results suggest that the simultaneous activity of a large dominant group of striatal output neurons is intimately associated with parkinsonian symptoms.

CaImAn an open source tool for scalable calcium imaging data analysis

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

The human brain contains billions of cells called neurons that rapidly carry information from one part of the brain to another. Progress in medical research and healthcare is hindered by the difficulty in understanding precisely which neurons are active at any given time. New brain imaging techniques and genetic tools allow researchers to track the activity of thousands of neurons in living animals over many months. However, these experiments produce large volumes of data that researchers currently have to analyze manually, which can take a long time and generate irreproducible results.

There is a need to develop new computational tools to analyze such data. The new tools should be able to operate on standard computers rather than just specialist equipment as this would limit the use of the solutions to particularly well-funded research teams. Ideally, the tools should also be able to operate in real-time as several experimental and therapeutic scenarios, like the control of robotic limbs, require this. To address this need, Giovannucci et al. developed a new software package called CaImAn to analyze brain images on a large scale.

Firstly, the team developed algorithms that are suitable to analyze large sets of data on laptops and other standard computing equipment. These algorithms were then adapted to operate online in real-time. To test how well the new software performs against manual analysis by human researchers, Giovannucci et al. asked several trained human annotators to identify active neurons that were round or donut-shaped in several sets of imaging data from mouse brains. Each set of data was independently analyzed by three or four researchers who then discussed any neurons they disagreed on to generate a ‘consensus annotation’. Giovannucci et al. then used CaImAn to analyze the same sets of data and compared the results to the consensus annotations. This demonstrated that CaImAn is nearly as good as human researchers at identifying active neurons in brain images.

CaImAn provides a quicker method to analyze large sets of brain imaging data and is currently used by over a hundred laboratories across the world. The software is open source, meaning that it is freely-available and that users are encouraged to customize it and collaborate with other users to develop it further.

Features of Neural Network Formation and Their Functions in Primary Hippocampal Cultures in the Context of Chronic TrkB Receptor System Influence

Discovering the mechanisms underlying homeostatic regulation in brain neural network formation and stability processes is one of the most urgent tasks in modern neuroscience. Brain-derived neurotrophic factor (BDNF) and the tropomyosin-related kinase B (TrkB) receptor system have long been considered the main regulators of neuronal survival and differentiation. The elucidation of methods for studying neural network activity makes investigating the complex mechanisms underlying neural network structure reorganization during development and detecting new mechanisms for neuronal activity remodeling possible. In this in vitro study, we investigated the effects of chronic BDNF (the main TrkB stimulator) and ANA-12 (a TrkB receptor system blocker) administration on the formation of neural-glial networks. The formation of spontaneous bioelectrical activity and functional neural structure depend on TrkB receptors, and blocking TrkB receptors inhibits full bioelectrical activity development. Cross-correlation analysis demonstrated the decisive role of TrkB in the formation and “strengths” of activity centers. Even though an appropriate ANA-12 concentration is non-toxic to nerve cells, numerous cells in culture medium containing this reagent do not exhibit metabolic activity and are not functionally involved in signal transmission processes. Electron microscopy studies revealed that chronically influencing the TrkB receptor system significantly alters synaptic and mitochondrial apparatus capture in cells, and functional analysis of mitochondrial activity confirmed these findings. Because knowledge of interactions between TrkB-mediated regulation and the mitochondrial state under normal conditions is rather limited, data on these relationships are particularly interesting and require further investigation. Thus, we assume that the molecular cascades mediated by TrkB actively participate in the formation of functionally complete brain neural networks.

Cholinergic modulation of striatal microcircuits

The purpose of this review is to bridge the gap between earlier literature on striatal cholinergic interneurons and mechanisms of microcircuit interaction demonstrated with the use of newly available tools. It is well known that the main source of the high level of acetylcholine in the striatum, compared to other brain regions, is the cholinergic interneurons. These interneurons provide an extensive local innervation that suggests they may be a key modulator of striatal microcircuits. Supporting this idea requires the consideration of functional properties of these interneurons, their influence on medium spiny neurons, other interneurons, and interactions with other synaptic regulators. Here, we underline the effects of intrastriatal and extrastriatal afferents onto cholinergic interneurons and discuss the activation of pre‐ and postsynaptic muscarinic and nicotinic receptors that participate in the modulation of intrastriatal neuronal interactions. We further address recent findings about corelease of other transmitters in cholinergic interneurons and actions of these interneurons in striosome and matrix compartments. In addition, we summarize recent evidence on acetylcholine‐mediated striatal synaptic plasticity and propose roles for cholinergic interneurons in normal striatal physiology. A short examination of their role in neurological disorders such as Parkinson's, Huntington's, and Tourette's pathologies and dystonia is also included.

Fast confocal fluorescence imaging in freely behaving mice

Fluorescence imaging in the brain of freely behaving mice is challenging due to severe miniaturization constraints. In particular, the ability to image a large field of view at high temporal resolution and with efficient out-of-focus background rejection still raises technical difficulties. Here, we present a novel fiberscope system that provides fast (up to 200 Hz) background-free fluorescence imaging in freely behaving mice over a field of view of diameter 230 μm. The fiberscope is composed of a custom-made multipoint-scanning confocal microscope coupled to the animal with an image guide and a micro-objective. By simultaneously registering a multipoint-scanning confocal image and a conventional widefield image, we subtracted the residual out-of-focus background and provided a background-free confocal image. Illumination and detection pinholes were created using a digital micromirror device, providing high adaptability to the sample structure and imaging conditions. Using this novel imaging tool, we demonstrated fast fluorescence imaging of microvasculature up to 120 μm deep in the mouse cortex, with an out-of-focus background reduced by two orders of magnitude compared with widefield microscopy. Taking advantage of the high acquisition rate (200 Hz), we measured red blood cell velocity in the cortical microvasculature and showed an increase in awake, unrestrained mice compared with anaesthetized animals.

Holographic imaging and photostimulation of neural activity

Optical imaging methods are powerful tools in neuroscience as they can systematically monitor the activity of neuronal populations with high spatiotemporal resolution using calcium or voltage indicators. Moreover, caged compounds and optogenetic actuators enable to optically manipulate neural activity. Among optical methods, computer-generated holography offers an enormous flexibility to sculpt the excitation light in three-dimensions (3D), particularly when combined with two-photon light sources. By projecting holographic light patterns on the sample, the activity of multiple neurons across a 3D brain volume can be simultaneously imaged or optically manipulated with single-cell precision. This flexibility makes two-photon holographic microscopy an ideal all-optical platform to simultaneously read and write activity in neuronal populations in vivo in 3D, a critical ability to dissect the function of neural circuits.

Contemporary strategies for dissecting the neuronal basis of neurodevelopmental disorders

Great efforts in clinical and basic research have shown progress in understanding the neurobiological mechanisms of neurodevelopmental disorders, such as autism, schizophrenia, and attention-deficit hyperactive disorders. Literature on this field have suggested that these disorders are affected by the complex interaction of genetic, biological, psychosocial and environmental risk factors. However, this complexity of interplaying risk factors during neurodevelopment has prevented a complete understanding of the causes of those neuropsychiatric symptoms. Recently, with advances in modern high-resolution neuroscience methods, the neural circuitry analysis approach has provided new solutions for understanding the causal relationship between dysfunction of a neural circuit and behavioral alteration in neurodevelopmental disorders. In this review we will discuss recent progress in developing novel optogenetic and chemogenetic strategies to investigate neurodevelopmental disorders.

Two-Photon Bidirectional Control and Imaging of Neuronal Excitability with High Spatial Resolution In Vivo

Sensory information is encoded within the brain in distributed spatiotemporal patterns of neuronal activity. Understanding how these patterns influence behavior requires a method to measure and to bidirectionally perturb with high spatial resolution the activity of the multiple neuronal cell types engaged in sensory processing. Here, we combined two-photon holography to stimulate neurons expressing blue light-sensitive opsins (ChR2 and GtACR2) with two-photon imaging of the red-shifted indicator jRCaMP1a in the mouse neocortex in vivo. We demonstrate efficient control of neural excitability across cell types and layers with holographic stimulation and improved spatial resolution by opsin somatic targeting. Moreover, we performed simultaneous two-photon imaging of jRCaMP1a and bidirectional two-photon manipulation of cellular activity with negligible effect of the imaging beam on opsin excitation. This all-optical approach represents a powerful tool to causally dissect how activity patterns in specified ensembles of neurons determine brain function and animal behavior.

Simultaneous two-photon imaging and two-photon optogenetics of cortical circuits in three dimensions

The simultaneous imaging and manipulating of neural activity could enable the functional dissection of neural circuits. Here we have combined two-photon optogenetics with simultaneous volumetric two-photon calcium imaging to measure and manipulate neural activity in mouse neocortex in vivo in three-dimensions (3D) with cellular resolution. Using a hybrid holographic approach, we simultaneously photostimulate more than 80 neurons over 150 μm in depth in layer 2/3 of the mouse visual cortex, while simultaneously imaging the activity of the surrounding neurons. We validate the usefulness of the method by photoactivating in 3D selected groups of interneurons, suppressing the response of nearby pyramidal neurons to visual stimuli in awake animals. Our all-optical approach could be used as a general platform to read and write neuronal activity.

Modern microscopy provides a window into the brain. The first light microscopes were able to magnify cells only in thin slices of tissue. By contrast, today’s light microscopes can image cells below the surface of the brain of a living animal. Even so, this remains challenging for several reasons. One is that the brain is three-dimensional. Another is that brain tissue scatters light. Trying to view neurons deep within the brain is a little like trying to view them through a glass of milk. Most of the light scatters on its way through the tissue with the result that little of the light reaches the target neurons.

Yang et al. have now tackled these challenges using a technique called holography. Holography produces 3D images of objects by splitting a beam of light and then recombining the beams in a specific way. Yang et al. applied this technique to an infrared laser beam, opting for infrared because it scatters much less in brain tissue than visible light. Directing each of the infrared beams to a different neuron can produce 3D images of multiple cells within the brain’s outer layer, the cortex, all at the same time.

The holographic infrared microscope can be used alongside two techniques called optogenetics and calcium imaging, in which light-sensitive proteins are inserted into neurons. Depending on the proteins introduced, shining light onto the neurons will either change their activity, or cause them to fluoresce whenever they are active. Just as a computer can both “read” and “write” data, the holographic microscope can thus read out existing neuronal activity or write new patterns of activity. By combining these techniques, Yang et al. were able to stimulate more than 80 neurons at the same time – and meanwhile visualize the activity of the surrounding neurons – at multiple depths within the mouse cortex.

This new microscopy technique, while a clear advance over existing methods, still cannot image and control neurons throughout the entire cortex. The next goal is to further extend this method across multiple brain areas and manipulate the activity of any subset of neurons at will. Neuroscientists will greatly benefit from the ability to image and alter the activity of living neural circuits in 3D. In the future, clinicians may be able to use this technique to treat brain disorders by adjusting the activity of abnormal neural circuits.