NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity

Jorstad, Anne; Blanc, Jérôme; Knott, Graham

doi:10.3389/fnana.2018.00059

Cited by 38 publications

(40 citation statements)

References 17 publications

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“…Three different compartments (soma, axons, and dendrites) were traced across the series of EM images. The measurements of length and volume were made using a NeuroMorph software toolset for 3D analysis of neurite morphology and connectivity (37). Synapses were identified by the symmetry of stained pre-and postsynaptic membranes and classified them into type I (asymmetric, excitatory) and type II (symmetric, inhibitory) types.…”

Section: In Vivo Electrophysiologymentioning

confidence: 99%

Somatostatin enhances visual processing and perception by suppressing excitatory inputs to parvalbumin-positive interneurons in V1

et al. 2020

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Somatostatin (SST) is a neuropeptide expressed in a major subtype of GABAergic interneurons in the cortex. Despite abundant expression of SST and its receptors, their modulatory function in cortical processing remains unclear. Here, we found that SST application in the primary visual cortex (V1) improves visual discrimination in freely moving mice and enhances orientation selectivity of V1 neurons. We also found that SST reduced excitatory synaptic transmission to parvalbumin-positive (PV+) fast-spiking interneurons but not to regular-spiking neurons. Last, using serial block-face scanning electron microscopy (SBEM), we found that axons of SST+ neurons in V1 often contact other axons that exhibit excitatory synapses onto the soma and proximal dendrites of the PV+ neuron. Collectively, our results demonstrate that the neuropeptide SST improves visual perception by enhancing visual gain of V1 neurons via a reduction in excitatory synaptic transmission to PV+ inhibitory neurons.

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Section: In Vivo Electrophysiologymentioning

confidence: 99%

Somatostatin enhances visual processing and perception by suppressing excitatory inputs to parvalbumin-positive interneurons in V1

et al. 2020

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“…Nevertheless, accurate 3D reconstructions can be used for quantitative morphometric analyses, rather than qualitative assessments of the 3D structures. Tools like NeuroMorph 19,20 and glycogen analysis 10 have been developed to take measurements on the 3D reconstructions for lengths, surface areas, and volumes, and on the distribution of cloud points, completely discarding the original EM stack 8,10 . Astrocytes represent an interesting case study, because the lack of visual clues or repetitive structural patterns give investigators a hint about the function of individual structural units and consequent lack of an adequate ontology of astrocytic processes 21 , make it challenging to design analytical tools.…”

Section: Introductionmentioning

confidence: 99%

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Calì

Kare

Agus

et al. 2019

JoVE

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Serial sectioning and subsequent high-resolution imaging of biological tissue using electron microscopy (EM) allow for the segmentation and reconstruction of high-resolution imaged stacks to reveal ultrastructural patterns that could not be resolved using 2D images. Indeed, the latter might lead to a misinterpretation of morphologies, like in the case of mitochondria; the use of 3D models is, therefore, more and more common and applied to the formulation of morphology-based functional hypotheses. To date, the use of 3D models generated from light or electron image stacks makes qualitative, visual assessments, as well as quantification, more convenient to be performed directly in 3D. As these models are often extremely complex, a virtual reality environment is also important to be set up to overcome occlusion and to take full advantage of the 3D structure. Here, a step-by-step guide from image segmentation to reconstruction and analysis is described in detail.

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“…The models were then exported as .obj files into the 3D modelling software (Blender; www.Blender.org). With the NeuroMorph tools plugin (Jorstad et al, 2015, 2018; neuromorph.epfl.ch), spine neck cross sectional area, spine neck length, and spine head volume were measured (Figure 1). Spine neck diameter was calculated from the average spine neck cross-sectional area.…”

Section: Methodsmentioning

confidence: 99%

Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation

Petersen

Knott

Tamada

et al. 2020

Preprint

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23Previously we showed that cryo fixation of brain tissue gave a truer 24 representation of brain ultrastructure in comparison with a standard 25 chemical fixation method (Korogod et al 2005). Extracellular space 26 matched physiological measurements, there were larger numbers of 27 docked vesicles and less glial coverage of synapses and blood 28 capillaries. Here, using the same preservation approaches we compared 29 the morphology of dendritic spines. We show that the length of the spine 30 and the volume of its head is unchanged, however, the spine neck width 31 is thinner by more than 30 % after cryo fixation. In addition, the weak 32 correlation between spine neck width and head volume seen after 33 chemical fixation was not present in cryo-fixed spines. Our data suggest 34 that spine neck geometry is independent of the spine head volume, with 35 cryo fixation showing enhanced spine head compartmentalization and a 36 higher predicted electrical resistance between spine head and parent 37 dendrite. 38 39 40 41 42 43 44 45 46 3 INTRODUCTION 47In our previous, parent paper (Korogod et al., 2015), we used a cryo fixation 48 method to study the neuropil of the adult mouse cerebral cortex, comparing it with 49 a standard chemical fixation approach that has been used for many years to 50 preserve the brain for analysis with electron microscopy (eg. Spacek and Harris, 51 1997; Knott et al., 2002). Korogod et al. (2015) found that cryo fixation appeared 52 to be able to preserve an extracellular space matching various previous in vivo 53 measurements, not found in chemically-fixed tissue. Furthermore, synapse 54 density and vesicle docking, as well as astrocytic processes close to synapses 55 and around blood capillaries, appeared to be significantly different between the 56 two fixation methods. This led us in this study to investigate the extent to which 57 dendritic spines might be affected by chemical fixation. 58The dendritic spine is a small dendritic protrusion that carries the majority 59 of the excitatory synaptic connections in the adult brain (Colonnier, 1968) with a 60 size and shape that is closely linked with its function (reviewed by: Holtmaat and 61 Svoboda, 2009; Harris and Kater, 1994). The larger the spine head, the larger its 62 synapse (Harris and Stevens, 1988, Arellano et al., 2007; Knott et al., 2006), the 63 number of its receptors (Kharazia et al., 1999; Nogochi et al., 2005; Nusser et al., 64 1998), and its synaptic strength (Matzusaki et al., 2001). However, the synapse 65 on the spine head is separated from the parent dendrite by the spine neck. This 66 is often thin, compartmentalizing biochemical signals and creating a potentially 67 significant electrical resistance between synapse and dendrite. Changes in the 68 morphology of spine head and neck have been seen after different forms of 69 activity including LTP induction and tetanic stimulation (Lang et al., 2004; 70 4 Matzusaki et al., 2004, Harvey and Svoboda, 2007; Tønnesen et al., 2014; 71 Fifkova and Anderson, 1981). The under...

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NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity

Cited by 38 publications

References 17 publications

Somatostatin enhances visual processing and perception by suppressing excitatory inputs to parvalbumin-positive interneurons in V1

Somatostatin enhances visual processing and perception by suppressing excitatory inputs to parvalbumin-positive interneurons in V1

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation

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