A comparison of manual neuronal reconstruction from biocytin histology or 2-photon imaging: morphometry and computer modeling

The developmental profile of visual cortex astrocytes

We investigated how astrocytes in layer 5 mouse visual cortex mature over postnatal days (P) 3-50. Across this age range, resting membrane potential increased, input resistance decreased, and membrane responses became more passive with age. Two-photon (2p) and confocal imaging of dye-loaded cells revealed that gap-junction coupling increased starting ∼P7. Morphological reconstructions revealed increased branch density but shorter branches after P20, suggesting that astrocyte branches may get pruned as tiling is established. Finally, we visualized spontaneous Ca²⁺ transients with 2p microscopy and found that Ca²⁺ events decorrelated, became more frequent and briefer with age. As astrocytes mature, spontaneous Ca²⁺ activity thus changes from relatively cell-wide, synchronous waves to local transients. Several astrocyte properties were stably mature from ∼P15, coinciding with eye opening, although morphology continued to develop. Our findings provide a descriptive foundation of astrocyte maturation, useful for the study of astrocytic impact on visual cortex critical period plasticity.

A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling

With advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, the Neuromorphological File Specification, available at www.mbfbioscience.com/filespecification (Angstman et al., 2020). The format, created and maintained by MBF Bioscience, is broadly utilized by the neuroscience community. The data format's structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological file format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data principles promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al., Scientific Data, 3, 160018,, 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream applications and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.

Microglial Metamorphosis in Three Dimensions in Virus Limbic Encephalitis: An Unbiased Pictorial Representation Based on a Stereological Sampling Approach of Surveillant and Reactive Microglia

Microglia influence pathological progression in neurological diseases, reacting to insults by expressing multiple morphofunctional phenotypes. However, the complete morphological spectrum of reactive microglia, as revealed by three-dimensional microscopic reconstruction, has not been detailed in virus limbic encephalitis. Here, using an anatomical series of brain sections, we expanded on an earlier Piry arbovirus encephalitis study to include CA1/CA2 and assessed the morphological response of homeostatic and reactive microglia at eight days post-infection. Hierarchical cluster and linear discriminant function analyses of multimodal morphometric features distinguished microglial morphology between infected animals and controls. For a broad representation of the spectrum of microglial morphology in each defined cluster, we chose representative cells of homeostatic and reactive microglia, using the sum of the distances of each cell in relation to all the others. Based on multivariate analysis, reactive microglia of infected animals showed more complex trees and thicker branches, covering a larger volume of tissue than in control animals. This approach offers a reliable representation of microglia dispersion in the Euclidean space, revealing the morphological kaleidoscope of surveillant and reactive microglia morphotypes. Because form precedes function in nature, our findings offer a starting point for research using integrative methods to understand microglia form and function.

Rare CASP6N73T variant associated with hippocampal volume exhibits decreased proteolytic activity, synaptic transmission defect, and neurodegeneration

Caspase-6 (Casp6) is implicated in Alzheimer disease (AD) cognitive impairment and pathology. Hippocampal atrophy is associated with cognitive impairment in AD. Here, a rare functional exonic missense CASP6 single nucleotide polymorphism (SNP), causing the substitution of asparagine with threonine at amino acid 73 in Casp6 (Casp6N73T), was associated with hippocampal subfield CA1 volume preservation. Compared to wild type Casp6 (Casp6WT), recombinant Casp6N73T altered Casp6 proteolysis of natural substrates Lamin A/C and α-Tubulin, but did not alter cleavage of the Ac-VEID-AFC Casp6 peptide substrate. Casp6N73T-transfected HEK293T cells showed elevated Casp6 mRNA levels similar to Casp6WT-transfected cells, but, in contrast to Casp6WT, did not accumulate active Casp6 subunits nor show increased Casp6 enzymatic activity. Electrophysiological and morphological assessments showed that Casp6N73T recombinant protein caused less neurofunctional damage and neurodegeneration in hippocampal CA1 pyramidal neurons than Casp6WT. Lastly, CASP6 mRNA levels were increased in several AD brain regions confirming the implication of Casp6 in AD. These studies suggest that the rare Casp6N73T variant may protect against hippocampal atrophy due to its altered catalysis of natural protein substrates and intracellular instability thus leading to less Casp6-mediated damage to neuronal structure and function.

Skeleton optimization of neuronal morphology based on three-dimensional shape restrictions

Background

Neurons are the basic structural unit of the brain, and their morphology is a key determinant of their classification. The morphology of a neuronal circuit is a fundamental component in neuron modeling. Recently, single-neuron morphologies of the whole brain have been used in many studies. The correctness and completeness of semimanually traced neuronal morphology are credible. However, there are some inaccuracies in semimanual tracing results. The distance between consecutive nodes marked by humans is very long, spanning multiple voxels. On the other hand, the nodes are marked around the centerline of the neuronal fiber, not on the centerline. Although these inaccuracies do not seriously affect the projection patterns that these studies focus on, they reduce the accuracy of the traced neuronal skeletons. These small inaccuracies will introduce deviations into subsequent studies that are based on neuronal morphology files.

Results

We propose a neuronal digital skeleton optimization method to evaluate and make fine adjustments to a digital skeleton after neuron tracing. Provided that the neuronal fiber shape is smooth and continuous, we describe its physical properties according to two shape restrictions. One restriction is designed based on the grayscale image, and the other is designed based on geometry. These two restrictions are designed to finely adjust the digital skeleton points to the neuronal fiber centerline. With this method, we design the three-dimensional shape restriction workflow of neuronal skeleton adjustment computation. The performance of the proposed method has been quantitatively evaluated using synthetic and real neuronal image data. The results show that our method can reduce the difference between the traced neuronal skeleton and the centerline of the neuronal fiber. Furthermore, morphology metrics such as the neuronal fiber length and radius become more precise.

Conclusions

This method can improve the accuracy of a neuronal digital skeleton based on traced results. The greater the accuracy of the digital skeletons that are acquired, the more precise the neuronal morphologies that are analyzed will be.

NeuroPath2Path: Classification and elastic morphing between neuronal arbors using path-wise similarity

Neuron shape and connectivity affect function. Modern imaging methods have proven successful at extracting morphological information. One potential path to achieve analysis of this morphology is through graph theory. Encoding by graphs enables the use of high throughput informatic methods to extract and infer brain function. However, the application of graph-theoretic methods to neuronal morphology comes with certain challenges in term of complex subgraph matching and the difficulty in computing intermediate shapes in between two imaged temporal samples. Here we report a novel, efficacious graph-theoretic method that rises to the challenges. The morphology of a neuron, which consists of its overall size, global shape, local branch patterns, and cell-specific biophysical properties, can vary significantly with the cell's identity, location, as well as developmental and physiological state. Various algorithms have been developed to customize shape based statistical and graph related features for quantitative analysis of neuromorphology, followed by the classification of neuron cell types using the features. Unlike the classical feature extraction based methods from imaged or 3D reconstructed neurons, we propose a model based on the rooted path decomposition from the soma to the dendrites of a neuron and extract morphological features from each constituent path. We hypothesize that measuring the distance between two neurons can be realized by minimizing the cost of continuously morphing the set of all rooted paths of one neuron to another. To validate this claim, we first establish the correspondence of paths between two neurons using a modified Munkres algorithm. Next, an elastic deformation framework that employs the square root velocity function is established to perform the continuous morphing, which, as an added benefit, provides an effective visualization tool. We experimentally show the efficacy of NeuroPath2Path, NeuroP2P, over the state of the art.

A Topological Representation of Branching Neuronal Morphologies

Many biological systems consist of branching structures that exhibit a wide variety of shapes. Our understanding of their systematic roles is hampered from the start by the lack of a fundamental means of standardizing the description of complex branching patterns, such as those of neuronal trees. To solve this problem, we have invented the Topological Morphology Descriptor (TMD), a method for encoding the spatial structure of any tree as a "barcode", a unique topological signature. As opposed to traditional morphometrics, the TMD couples the topology of the branches with their spatial extents by tracking their topological evolution in 3-dimensional space. We prove that neuronal trees, as well as stochastically generated trees, can be accurately categorized based on their TMD profiles. The TMD retains sufficient global and local information to create an unbiased benchmark test for their categorization and is able to quantify and characterize the structural differences between distinct morphological groups. The use of this mathematically rigorous method will advance our understanding of the anatomy and diversity of branching morphologies.

N3DFix: an Algorithm for Automatic Removal of Swelling Artifacts in Neuronal Reconstructions

It is well established that not only electrophysiology but also morphology plays an important role in shaping the functional properties of neurons. In order to properly quantify morphological features it is first necessary to translate observational histological data into 3-dimensional geometric reconstructions of the neuronal structures. This reconstruction process, independently of being manual or (semi-)automatic, requires several preparation steps (e.g. histological processing) before data acquisition using specialized software. Unfortunately these processing steps likely produce artifacts which are then carried to the reconstruction, such as tissue shrinkage and formation of swellings. If not accounted for and corrected, these artifacts can change significantly the results from morphometric analysis and computer simulations. Here we present N3DFix, an open-source software which uses a correction algorithm to automatically find and fix swelling artifacts in neuronal reconstructions. N3DFix works as a post-processing tool and therefore can be used in either manual or (semi-)automatic reconstructions. The algorithm's internal parameters have been defined using a "ground truth" dataset produced by a neuroanatomist, involving two complementary manual reconstruction procedures: in the first, neuronal topology was faithfully reconstructed, including all swelling artifacts; in the second procedure a meticulous correction of the artifacts was manually performed directly during neuronal tracing. The internal parameters of N3DFix were set to minimize the differences between manual amendments and the algorithm's corrections. It is shown that the performance of N3DFix is comparable to careful manual correction of the swelling artifacts. To promote easy access and wide adoption, N3DFix is available in NEURON, Vaa3D and Py3DN.

Morphology of Dbx1 respiratory neurons in the preBötzinger complex and reticular formation of neonatal mice

The relationship between neuron morphology and function is a perennial issue in neuroscience. Information about synaptic integration, network connectivity, and the specific roles of neuronal subpopulations can be obtained through morphological analysis of key neurons within a microcircuit. Here we present morphologies of two classes of brainstem respiratory neurons. First, interneurons derived from Dbx1-expressing precursors (Dbx1 neurons) in the preBötzinger complex (preBötC) of the ventral medulla that generate the rhythm for inspiratory breathing movements. Second, Dbx1 neurons of the intermediate reticular formation that influence the motor pattern of pharyngeal and lingual movements during the inspiratory phase of the breathing cycle. We describe the image acquisition and subsequent digitization of morphologies of respiratory Dbx1 neurons from the preBötC and the intermediate reticular formation that were first recorded in vitro. These data can be analyzed comparatively to examine how morphology influences the roles of Dbx1 preBötC and Dbx1 reticular interneurons in respiration and can also be utilized to create morphologically accurate compartmental models for simulation and modeling of respiratory circuits.

Dendritic Arborization Patterns of Small Juxtaglomerular Cell Subtypes within the Rodent Olfactory Bulb

Within the glomerular layer of the rodent olfactory bulb, numerous subtypes of local interneurons contribute to early processing of incoming sensory information. Here we have investigated dopaminergic and other small local juxtaglomerular cells in rats and mice and characterized their dendritic arborization pattern with respect to individual glomeruli by fluorescent labeling via patching and reconstruction of dendrites and glomerular contours from two-photon imaging data. Dopaminergic neurons were identified in a transgenic mouse line where the expression of dopamine transporter (DAT) was labeled with GFP. Among the DAT+ cells we found a small short-axon cell (SAC) subtype featuring hitherto undescribed dendritic specializations. These densely ramifying structures clasped mostly around somata of other juxtaglomerular neurons, which were also small, non-dopaminergic and to a large extent non-GABAergic. Clasping SACs were observed also in wild-type mice and juvenile rats. In DAT+ SAC dendrites, single backpropagating action potentials evoked robust calcium entry throughout both clasping and non-clasping compartments. Besides clasping SACs, most other small neurons either corresponded to the classical periglomerular cell type (PGCs), which was never DAT+, or were undersized cells with a small dendritic tree and low excitability. Aside from the presence of clasps in SAC dendrites, many descriptors of dendritic morphology such as the number of dendrites and the extent of branching were not significantly different between clasping SACs and PGCs. However, a detailed morphometric analysis in relation to glomerular contours revealed that the dendrites of clasping SACs arborized mostly in the juxtaglomerular space and never entered more than one glomerulus (if at all), whereas most PGC dendrites were restricted to their parent glomerulus, similar to the apical tufts of mitral cells. These complementary arborization patterns might underlie a highly complementary functional connectivity. The morphometric approach may serve to differentiate also other subtypes of juxtaglomerular neurons, help to identify putative synaptic partners and thus to establish a more refined picture of glomerular network interactions during odor sensing.

AII amacrine cells: quantitative reconstruction and morphometric analysis of electrophysiologically identified cells in live rat retinal slices imaged with multi-photon excitation microscopy

AII amacrine cells have been found in all mammalian retinas examined and play an important role for visual processing under both scotopic and photopic conditions. Whereas ultrastructural investigations have provided a detailed understanding of synaptic connectivity, there is little information available with respect to quantitative properties and variation of cellular morphology. Here, we performed whole-cell recordings from AII amacrine cells in rat retinal slices and filled the cells with fluorescent dyes. Multi-photon excitation microscopy was used to acquire image stacks and after deconvolution, we performed quantitative morphological reconstruction by computer-aided manual tracing. We reconstructed and performed morphometric analysis on 43 AII amacrine cells, with a focus on branching pattern, dendritic lengths and diameters, surface area, and number and distribution of dendritic varicosities. Compared to previous descriptions, the most surprising result was the considerable extent of branching, with the maximum branch order ranging from approximately 10-40. We found that AII amacrine cells conform to a recently described general structural design principle for neural arbors, where arbor density decreases proportionally to increasing territory size. We confirmed and quantified the bi-stratified morphology of AII amacrine cells by analyzing the arborizations as a function of retinal localization or with Sholl spheres. Principal component and cluster analysis revealed no evidence for morphological subtypes of AII amacrines. These results establish a database of morphometric properties important for studies of development, regeneration, degeneration, and disease processes, as well as a workflow compatible with compartmental modeling.

Clusters of synaptic inputs on dendrites of layer 5 pyramidal cells in mouse visual cortex

The spatial organization of synaptic inputs on the dendritic tree of cortical neurons plays a major role for dendritic integration and neural computations, yet, remarkably little is known about it. We mapped the spatial organization of glutamatergic synapses between layer 5 pyramidal cells by combining optogenetics and 2-photon calcium imaging in mouse neocortical slices. To mathematically characterize the organization of inputs we developed an approach based on combinatorial analysis of the likelihoods of specific synapse arrangements. We found that the synapses of intralaminar inputs form clusters on the basal dendrites of layer 5 pyramidal cells. These clusters contain 4 to 14 synapses within ≤30 µm of dendrite. According to the spatiotemporal characteristics of synaptic summation, these numbers suggest that there will be non-linear dendritic integration of synaptic inputs during synchronous activation.

DOI:http://dx.doi.org/10.7554/eLife.09222.001

Neurons in the brain exchange information through points of contact called synapses. If electrical activity arriving at a number of synapses exceeds a certain threshold, it can trigger an electrical impulse, which is transmitted to the next neuron. Synapses generally connect with branch-like structures called dendrites on the receiving neuron. However, little is known about how synapses are arranged on dendrites.

Gökçe et al. have now used a technique called optogenetics to work out the exact arrangement of a type of synapse on neurons in a part of the mouse brain that is devoted to vision. Optogenetics takes advantage of light-activated proteins that can trigger electrical activity. Gökçe et al. used mice that had been genetically engineered to produce these proteins in specific neurons, and then deliberately triggered electrical activity simply by shining light on these neurons. The experiments also used another technique called two-photon calcium imaging to monitor the activity of single synapses in response to the electrical activity triggered by optogenetics.

Gökçe et al. found that these neurons have clusters of four to fourteen synapses within a space of 30 micrometers along a dendrite. Synapses in clusters that are active at the same time can interact and thereby generate electrical signals more effectively than synapses spread across the dendrites. Further experiments are now needed to map the synapses between other kinds of neurons, and to map synapses from two different inputs at the same time.

DOI:http://dx.doi.org/10.7554/eLife.09222.002

Using Multiple Whole-Cell Recordings to Study Spike-Timing-Dependent Plasticity in Acute Neocortical Slices

This protocol provides a method for quadruple whole-cell recording to study synaptic plasticity of neocortical connections, with a special focus on spike-timing-dependent plasticity (STDP). It also describes how to morphologically identify recorded cells from two-photon laser-scanning microscopy (2PLSM) stacks.

In Vitro Investigation of Synaptic Plasticity

A classical in vitro model for investigation of information storage in the brain is based on the acute hippocampal slice. Here, repeated high-frequency stimulation of excitatory Schaeffer collaterals making synapses onto pyramidal cells in the hippocampal CA1 region leads to strengthening of evoked field-recording responses-long-term potentiation (LTP)-in keeping with Hebb's postulate. This model remains tremendously influential for its reliability, specificity, and relative ease of use. More recent plasticity studies have explored various other brain regions including the neocortex, which often requires more laborious whole-cell recordings of synaptically connected pairs of neurons, to ensure that the identities of recorded cells are known. In addition, with this experimental approach, the spiking activity can be controlled with millisecond precision, which is necessary for the study of spike-timing-dependent plasticity (STDP). Here, we provide protocols for in vitro study of hippocampal CA1 LTP using field recordings, and of STDP in synaptically connected pairs of layer-5 pyramidal cells in acute slices of rodent neocortex.

Synapse-specific expression of calcium-permeable AMPA receptors in neocortical layer 5

Key points

In the hippocampus, calcium‐permeable AMPA receptors have been found in a restricted subset of neuronal types that inhibit other neurons, although their localization in the neocortex is less well understood.

In the present study, we looked for calcium‐permeable AMPA receptors in two distinct populations of neocortical inhibitory neurons: basket cells and Martinotti cells. We found them in the former but not in the latter. Furthermore, in basket cells, these receptors were associated with particularly fast responses.

Computer modelling predicted (and experiments verified) that fast calcium‐permeable AMPA receptors enable basket cells to respond rapidly, such that they promptly inhibit neighbouring cells and shut down activity.

The results obtained in the present study help our understanding of pathologies such as stroke and epilepsy that have been associated with disordered regulation of calcium‐permeable AMPA receptors.

Abstract

AMPA‐type glutamate receptors (AMPARs) lacking an edited GluA2 subunit are calcium‐permeable (CP) and contribute to synaptic plasticity in several hippocampal interneuron types, although their precise role in the neocortex is not well described. We explored the presence of CP‐AMPARs at pyramidal cell (PC) inputs to Martinotti cells (MCs) and basket cells (BCs) in layer 5 of the developing mouse visual cortex (postnatal days 12–21). GluA2 immunolabelling was stronger in MCs than in BCs. A differential presence of CP‐AMPARs at PC‐BC and PC‐MC synapses was confirmed electrophysiologically, based on measures of spermine‐dependent rectification and CP‐AMPAR blockade by 1‐naphtyl acetyl spermine using recordings from synaptically connected cell pairs, NPEC‐AMPA uncaging and miniature current recordings. In addition, CP‐AMPAR expression in BCs was correlated with rapidly decaying synaptic currents. Computer modelling predicted that this reduces spike latencies and sharpens suprathreshold responses in BCs, which we verified experimentally using the dynamic clamp technique. Thus, the synapse‐specific expression of CP‐AMPARs may critically influence both plasticity and information processing in neocortical microcircuits.

In the hippocampus, calcium‐permeable AMPA receptors have been found in a restricted subset of neuronal types that inhibit other neurons, although their localization in the neocortex is less well understood.

In the present study, we looked for calcium‐permeable AMPA receptors in two distinct populations of neocortical inhibitory neurons: basket cells and Martinotti cells. We found them in the former but not in the latter. Furthermore, in basket cells, these receptors were associated with particularly fast responses.

Computer modelling predicted (and experiments verified) that fast calcium‐permeable AMPA receptors enable basket cells to respond rapidly, such that they promptly inhibit neighbouring cells and shut down activity.

The results obtained in the present study help our understanding of pathologies such as stroke and epilepsy that have been associated with disordered regulation of calcium‐permeable AMPA receptors.