Serialelectron microscopy imaging is crucial for exploring the structure of cells and tissues. The development of block face scanning electron microscopy methods and their ability to capture large image stacks, some with near isotropic voxels, is proving particularly useful for the exploration of brain tissue. This has led to the creation of numerous algorithms and software for segmenting out different features from the image stacks. However, there are few tools available to view these results and make detailed morphometric analyses on all, or part, of these 3D models. We have addressed this issue by constructing a collection of software tools, called NeuroMorph, with which users can view the segmentation results, in conjunction with the original image stack, manipulate these objects in 3D, and make measurements of any region. This approach to collecting morphometric data provides a faster means of analysing the geometry of structures, such as dendritic spines and axonal boutons. This bridges the gap that currently exists between rapid reconstruction techniques, offered by computer vision research, and the need to collect measurements of shape and form from segmented structures that is currently done using manual segmentation methods.

This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.

Abstract. We describe a system dedicated to the analysis of the complex threedimensional anatomy and dynamics of an abnormal heart mitral valve using three-dimensional echocardiography to characterize the valve pathophysiology. This system is intended to aid cardiothoracic surgeons in conducting preoperative surgical planning and in understanding the outcome of "virtual" mitral valve repairs. This paper specifically addresses the analysis of threedimensional transesophageal echocardiographic imagery to recover the valve structure and predict the competency of a surgically modified valve by computing its closed state from an assumed open configuration. We report on a 3D TEE structure recovery method and a mechanical modeling approach used for the valve modeling and simulation.

The geometries of axons, dendrites and their synaptic connections provide important information about their functional properties. These can be collected directly from measurements made on serial electron microscopy images. However, manual and automated segmentation methods can also yield large and accurate models of neuronal architecture from which morphometric data can be gathered in 3D space. This technical paper presents a series of software tools, operating in the Blender open source software, for the quantitative analysis of axons and their synaptic connections. These allow the user to annotate serial EM images to generate models of different cellular structures, or to make measurements of models generated in other software. The paper explains how the tools can measure the cross-sectional surface area at regular intervals along the length of an axon, and the amount of contact with other cellular elements in the surrounding neuropil, as well as the density of organelles, such as vesicles and mitochondria, that it contains. Nearest distance measurements, in 3D space, can also be made between any features. This provides many capabilities such as the detection of boutons and the evaluation of different vesicle pool sizes, allowing users to comprehensively describe many aspects of axonal morphology and connectivity.

The ability to measure minute structural changes in neural circuits is essential for long-term in vivo imaging studies. Here, we propose a methodology for detection and measurement of structural changes in axonal boutons imaged with time-lapse two-photon laser scanning microscopy (2PLSM). Correlative 2PLSM and 3D electron microscopy (EM) analysis, performed in mouse barrel cortex, showed that the proposed method has low fractions of false positive/negative bouton detections (2/0 out of 18), and that 2PLSM-based bouton weights are correlated with their volumes measured in EM (r = 0.93). Next, the method was applied to a set of axons imaged in quick succession to characterize measurement uncertainty. The results were used to construct a statistical model in which bouton addition, elimination, and size changes are described probabilistically, rather than being treated as deterministic events. Finally, we demonstrate that the model can be used to quantify significant structural changes in boutons in long-term imaging experiments.