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The anatomical problem posed by brain complexity and size: a potential solution.

DeFelipe J - Front Neuroanat (2015)

Bottom Line: Over the years the field of neuroanatomy has evolved considerably but unraveling the extraordinary structural and functional complexity of the brain seems to be an unattainable goal, partly due to the fact that it is only possible to obtain an imprecise connection matrix of the brain.The reasons why reaching such a goal appears almost impossible to date is discussed here, together with suggestions of how we could overcome this anatomical problem by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration.Generating a realistic computational model seems to be the solution rather than attempting to fully reconstruct the whole brain or a particular brain region.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio Cajal de Circuitos Corticales (Centro de Tecnología Biomédica: UPM), Instituto Cajal (CSIC) and CIBERNED Madrid, Spain.

ABSTRACT
Over the years the field of neuroanatomy has evolved considerably but unraveling the extraordinary structural and functional complexity of the brain seems to be an unattainable goal, partly due to the fact that it is only possible to obtain an imprecise connection matrix of the brain. The reasons why reaching such a goal appears almost impossible to date is discussed here, together with suggestions of how we could overcome this anatomical problem by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration. Generating a realistic computational model seems to be the solution rather than attempting to fully reconstruct the whole brain or a particular brain region.

No MeSH data available.


Reconstruction of a minicolumn. (A) Schematic representation of a minicolumn in which only the soma and proximal dendrites of pyramidal cells (black) and the main axon (blue) are represented. Note that the axons form bundles due to the vertical arrangement of pyramidal cells. (B) The apical dendrites also form vertical bundles and, although variability exists both between cortical areas and species in the size and number of dendrites that form the bundles as well as in the layer where the terminal dendritic tufts terminate, in general, the vertical dendritic organization is as follows. As reviewed in DeFelipe (2005), distinct bundles of pyramidal neuron apical dendrites are formed in different levels of layer V, and ascend towards the pial surface. Apical dendrites originating from pyramidal cells in layers II–III mainly join the bundle periphery. At this level, the apical dendrites of layer V and layer II–III pyramidal neurons begin to form terminal tufts which end in layer I. By contrast, the apical dendrites originating from Layer VI pyramidal cells do not join the layer V bundles, but are arranged as separate bundles which ascend to layer IV and form terminal tufts there. The core of the long dendritic bundles that extend from layer V to layers II–III is therefore principally composed of the apical dendrites pertaining to layer V pyramidal neurons. (C) Image captured by focused ion beam milling and scanning electron microscopy (FIB/SEM) to show the relatively high density of synapses in the neuropil and the ultrastructural appearance of asymmetric and symmetric synapses in the rat cerebral cortex. Four asymmetric synapses (arrows) and one symmetric synapse (arrowhead) can be identified on four dendritic spines (d1 to d4). Asymmetric synapses show a thick post-synaptic density. The symmetric synapse has a thin post-synaptic density, which is similar to the pre-synaptic density, and is located on the neck of a dendritic spine (d1). Scale bar, 500 nm. (D–G) Three-dimensional representation of a stack of serial sections and the synaptic profiles that appear in the corresponding counting brick. (D,E) show a stack of serial sections, slightly rotated counter-clockwise through the vertical axis in (E). Only 12 sections are shown out of the 115 that compose the complete stack. An unbiased counting frame was drawn on each section, taking the green and the red lines as the acceptance and exclusion boundaries, respectively. To extend the counting frame to three dimensions, the front section was considered as an acceptance plane and the last section as an exclusion plane. Thus, synaptic profiles (contours of the synaptic membrane densities) were counted inside an unbiased counting brick bound by three acceptance planes (top, left and front) and three exclusion planes (right, bottom and back). As an example, the 10 synaptic profiles that appeared in the first section (acceptance plane), without intersecting any of the exclusion planes, have been numbered from 1 to 10 in (D,E). The counting frame measured 6.86 × 5.28 μm after correction for tissue shrinkage. In (F,G) the counting brick and the three dimensional reconstructions of synaptic profiles have been rendered. Green objects represent asymmetric synaptic profiles and red objects symmetric synaptic profiles. All the objects shown were inside the counting brick or intersected one of the acceptance boundaries, without intersecting any of the exclusion planes. Numbered objects correspond to the same synaptic profiles shown in (D,E). Note that every object can be individually identified and localized in the 3D space. Panels (A,B) have been adapted from DeFelipe (2005), and (C–G) and legend have been taken from Merchán-Pérez et al. (2009).
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Figure 3: Reconstruction of a minicolumn. (A) Schematic representation of a minicolumn in which only the soma and proximal dendrites of pyramidal cells (black) and the main axon (blue) are represented. Note that the axons form bundles due to the vertical arrangement of pyramidal cells. (B) The apical dendrites also form vertical bundles and, although variability exists both between cortical areas and species in the size and number of dendrites that form the bundles as well as in the layer where the terminal dendritic tufts terminate, in general, the vertical dendritic organization is as follows. As reviewed in DeFelipe (2005), distinct bundles of pyramidal neuron apical dendrites are formed in different levels of layer V, and ascend towards the pial surface. Apical dendrites originating from pyramidal cells in layers II–III mainly join the bundle periphery. At this level, the apical dendrites of layer V and layer II–III pyramidal neurons begin to form terminal tufts which end in layer I. By contrast, the apical dendrites originating from Layer VI pyramidal cells do not join the layer V bundles, but are arranged as separate bundles which ascend to layer IV and form terminal tufts there. The core of the long dendritic bundles that extend from layer V to layers II–III is therefore principally composed of the apical dendrites pertaining to layer V pyramidal neurons. (C) Image captured by focused ion beam milling and scanning electron microscopy (FIB/SEM) to show the relatively high density of synapses in the neuropil and the ultrastructural appearance of asymmetric and symmetric synapses in the rat cerebral cortex. Four asymmetric synapses (arrows) and one symmetric synapse (arrowhead) can be identified on four dendritic spines (d1 to d4). Asymmetric synapses show a thick post-synaptic density. The symmetric synapse has a thin post-synaptic density, which is similar to the pre-synaptic density, and is located on the neck of a dendritic spine (d1). Scale bar, 500 nm. (D–G) Three-dimensional representation of a stack of serial sections and the synaptic profiles that appear in the corresponding counting brick. (D,E) show a stack of serial sections, slightly rotated counter-clockwise through the vertical axis in (E). Only 12 sections are shown out of the 115 that compose the complete stack. An unbiased counting frame was drawn on each section, taking the green and the red lines as the acceptance and exclusion boundaries, respectively. To extend the counting frame to three dimensions, the front section was considered as an acceptance plane and the last section as an exclusion plane. Thus, synaptic profiles (contours of the synaptic membrane densities) were counted inside an unbiased counting brick bound by three acceptance planes (top, left and front) and three exclusion planes (right, bottom and back). As an example, the 10 synaptic profiles that appeared in the first section (acceptance plane), without intersecting any of the exclusion planes, have been numbered from 1 to 10 in (D,E). The counting frame measured 6.86 × 5.28 μm after correction for tissue shrinkage. In (F,G) the counting brick and the three dimensional reconstructions of synaptic profiles have been rendered. Green objects represent asymmetric synaptic profiles and red objects symmetric synaptic profiles. All the objects shown were inside the counting brick or intersected one of the acceptance boundaries, without intersecting any of the exclusion planes. Numbered objects correspond to the same synaptic profiles shown in (D,E). Note that every object can be individually identified and localized in the 3D space. Panels (A,B) have been adapted from DeFelipe (2005), and (C–G) and legend have been taken from Merchán-Pérez et al. (2009).

Mentions: Electron microscopy with serial section reconstruction is the favored method for tracing the synaptome, and this technology has a proven track record for acquiring 3D data from ultrathin sections. However, it is exceedingly time-consuming and challenging to obtain long series of such sections. As a result, the reconstruction of large tissue volumes is usually not possible. The recent development of automated or semi-automated electron microscopy techniques (which require much less labor-intensive human interaction and training than conventional electron microcopy) represents an important advance in the study of the synaptome (Denk and Horstmann, 2004; Smith, 2007; Helmstaedter et al., 2008; Knott et al., 2008; Merchán-Pérez et al., 2009). For example, the 3D reconstruction method involving the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM; Figures 3D–G) permits the rapid and automatic serial reconstruction of relatively large tissue volumes (Knott et al., 2008; Merchán-Pérez et al., 2009). Nevertheless, even using this FIB/SEM technology, full reconstruction of whole brains will only be possible in some invertebrates or for relatively simple nervous systems. Indeed, even for a small mammal like the mouse, it is impossible to fully reconstruct the brain at the ultrastructural level since the magnification needed to visualize synapses yields relatively small images (in the order tens of μm2).


The anatomical problem posed by brain complexity and size: a potential solution.

DeFelipe J - Front Neuroanat (2015)

Reconstruction of a minicolumn. (A) Schematic representation of a minicolumn in which only the soma and proximal dendrites of pyramidal cells (black) and the main axon (blue) are represented. Note that the axons form bundles due to the vertical arrangement of pyramidal cells. (B) The apical dendrites also form vertical bundles and, although variability exists both between cortical areas and species in the size and number of dendrites that form the bundles as well as in the layer where the terminal dendritic tufts terminate, in general, the vertical dendritic organization is as follows. As reviewed in DeFelipe (2005), distinct bundles of pyramidal neuron apical dendrites are formed in different levels of layer V, and ascend towards the pial surface. Apical dendrites originating from pyramidal cells in layers II–III mainly join the bundle periphery. At this level, the apical dendrites of layer V and layer II–III pyramidal neurons begin to form terminal tufts which end in layer I. By contrast, the apical dendrites originating from Layer VI pyramidal cells do not join the layer V bundles, but are arranged as separate bundles which ascend to layer IV and form terminal tufts there. The core of the long dendritic bundles that extend from layer V to layers II–III is therefore principally composed of the apical dendrites pertaining to layer V pyramidal neurons. (C) Image captured by focused ion beam milling and scanning electron microscopy (FIB/SEM) to show the relatively high density of synapses in the neuropil and the ultrastructural appearance of asymmetric and symmetric synapses in the rat cerebral cortex. Four asymmetric synapses (arrows) and one symmetric synapse (arrowhead) can be identified on four dendritic spines (d1 to d4). Asymmetric synapses show a thick post-synaptic density. The symmetric synapse has a thin post-synaptic density, which is similar to the pre-synaptic density, and is located on the neck of a dendritic spine (d1). Scale bar, 500 nm. (D–G) Three-dimensional representation of a stack of serial sections and the synaptic profiles that appear in the corresponding counting brick. (D,E) show a stack of serial sections, slightly rotated counter-clockwise through the vertical axis in (E). Only 12 sections are shown out of the 115 that compose the complete stack. An unbiased counting frame was drawn on each section, taking the green and the red lines as the acceptance and exclusion boundaries, respectively. To extend the counting frame to three dimensions, the front section was considered as an acceptance plane and the last section as an exclusion plane. Thus, synaptic profiles (contours of the synaptic membrane densities) were counted inside an unbiased counting brick bound by three acceptance planes (top, left and front) and three exclusion planes (right, bottom and back). As an example, the 10 synaptic profiles that appeared in the first section (acceptance plane), without intersecting any of the exclusion planes, have been numbered from 1 to 10 in (D,E). The counting frame measured 6.86 × 5.28 μm after correction for tissue shrinkage. In (F,G) the counting brick and the three dimensional reconstructions of synaptic profiles have been rendered. Green objects represent asymmetric synaptic profiles and red objects symmetric synaptic profiles. All the objects shown were inside the counting brick or intersected one of the acceptance boundaries, without intersecting any of the exclusion planes. Numbered objects correspond to the same synaptic profiles shown in (D,E). Note that every object can be individually identified and localized in the 3D space. Panels (A,B) have been adapted from DeFelipe (2005), and (C–G) and legend have been taken from Merchán-Pérez et al. (2009).
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Figure 3: Reconstruction of a minicolumn. (A) Schematic representation of a minicolumn in which only the soma and proximal dendrites of pyramidal cells (black) and the main axon (blue) are represented. Note that the axons form bundles due to the vertical arrangement of pyramidal cells. (B) The apical dendrites also form vertical bundles and, although variability exists both between cortical areas and species in the size and number of dendrites that form the bundles as well as in the layer where the terminal dendritic tufts terminate, in general, the vertical dendritic organization is as follows. As reviewed in DeFelipe (2005), distinct bundles of pyramidal neuron apical dendrites are formed in different levels of layer V, and ascend towards the pial surface. Apical dendrites originating from pyramidal cells in layers II–III mainly join the bundle periphery. At this level, the apical dendrites of layer V and layer II–III pyramidal neurons begin to form terminal tufts which end in layer I. By contrast, the apical dendrites originating from Layer VI pyramidal cells do not join the layer V bundles, but are arranged as separate bundles which ascend to layer IV and form terminal tufts there. The core of the long dendritic bundles that extend from layer V to layers II–III is therefore principally composed of the apical dendrites pertaining to layer V pyramidal neurons. (C) Image captured by focused ion beam milling and scanning electron microscopy (FIB/SEM) to show the relatively high density of synapses in the neuropil and the ultrastructural appearance of asymmetric and symmetric synapses in the rat cerebral cortex. Four asymmetric synapses (arrows) and one symmetric synapse (arrowhead) can be identified on four dendritic spines (d1 to d4). Asymmetric synapses show a thick post-synaptic density. The symmetric synapse has a thin post-synaptic density, which is similar to the pre-synaptic density, and is located on the neck of a dendritic spine (d1). Scale bar, 500 nm. (D–G) Three-dimensional representation of a stack of serial sections and the synaptic profiles that appear in the corresponding counting brick. (D,E) show a stack of serial sections, slightly rotated counter-clockwise through the vertical axis in (E). Only 12 sections are shown out of the 115 that compose the complete stack. An unbiased counting frame was drawn on each section, taking the green and the red lines as the acceptance and exclusion boundaries, respectively. To extend the counting frame to three dimensions, the front section was considered as an acceptance plane and the last section as an exclusion plane. Thus, synaptic profiles (contours of the synaptic membrane densities) were counted inside an unbiased counting brick bound by three acceptance planes (top, left and front) and three exclusion planes (right, bottom and back). As an example, the 10 synaptic profiles that appeared in the first section (acceptance plane), without intersecting any of the exclusion planes, have been numbered from 1 to 10 in (D,E). The counting frame measured 6.86 × 5.28 μm after correction for tissue shrinkage. In (F,G) the counting brick and the three dimensional reconstructions of synaptic profiles have been rendered. Green objects represent asymmetric synaptic profiles and red objects symmetric synaptic profiles. All the objects shown were inside the counting brick or intersected one of the acceptance boundaries, without intersecting any of the exclusion planes. Numbered objects correspond to the same synaptic profiles shown in (D,E). Note that every object can be individually identified and localized in the 3D space. Panels (A,B) have been adapted from DeFelipe (2005), and (C–G) and legend have been taken from Merchán-Pérez et al. (2009).
Mentions: Electron microscopy with serial section reconstruction is the favored method for tracing the synaptome, and this technology has a proven track record for acquiring 3D data from ultrathin sections. However, it is exceedingly time-consuming and challenging to obtain long series of such sections. As a result, the reconstruction of large tissue volumes is usually not possible. The recent development of automated or semi-automated electron microscopy techniques (which require much less labor-intensive human interaction and training than conventional electron microcopy) represents an important advance in the study of the synaptome (Denk and Horstmann, 2004; Smith, 2007; Helmstaedter et al., 2008; Knott et al., 2008; Merchán-Pérez et al., 2009). For example, the 3D reconstruction method involving the combination of focused ion beam milling and scanning electron microscopy (FIB/SEM; Figures 3D–G) permits the rapid and automatic serial reconstruction of relatively large tissue volumes (Knott et al., 2008; Merchán-Pérez et al., 2009). Nevertheless, even using this FIB/SEM technology, full reconstruction of whole brains will only be possible in some invertebrates or for relatively simple nervous systems. Indeed, even for a small mammal like the mouse, it is impossible to fully reconstruct the brain at the ultrastructural level since the magnification needed to visualize synapses yields relatively small images (in the order tens of μm2).

Bottom Line: Over the years the field of neuroanatomy has evolved considerably but unraveling the extraordinary structural and functional complexity of the brain seems to be an unattainable goal, partly due to the fact that it is only possible to obtain an imprecise connection matrix of the brain.The reasons why reaching such a goal appears almost impossible to date is discussed here, together with suggestions of how we could overcome this anatomical problem by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration.Generating a realistic computational model seems to be the solution rather than attempting to fully reconstruct the whole brain or a particular brain region.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio Cajal de Circuitos Corticales (Centro de Tecnología Biomédica: UPM), Instituto Cajal (CSIC) and CIBERNED Madrid, Spain.

ABSTRACT
Over the years the field of neuroanatomy has evolved considerably but unraveling the extraordinary structural and functional complexity of the brain seems to be an unattainable goal, partly due to the fact that it is only possible to obtain an imprecise connection matrix of the brain. The reasons why reaching such a goal appears almost impossible to date is discussed here, together with suggestions of how we could overcome this anatomical problem by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration. Generating a realistic computational model seems to be the solution rather than attempting to fully reconstruct the whole brain or a particular brain region.

No MeSH data available.