The authors would like to thank the donors and their families for their generous gift. Thank you to Mr. Xiao Xuan Li who recorded the video and helped with video editing; Ms. Hannah Lewis and Mr. Louis Szabo for providing technical support; and Professor Jan Provis for reviewing the video and providing input to the video content.

All methods described here have been approved by the Human Research Ethics Committee of the Australian National University. To create the ventricular model we used the Klingler fiber dissection technique12,14. The Klingler technique is a tactile dissection method that involves removing small portions of the gray matter of the cortex and peeling off bundles of nerve fibers, thus providing a step-by-step guide through the tissue layers from the surface to the deep structures of the brain.
NOTE: The brain specimen used to demonstrate this protocol in the accompanying video and images was carefully removed from a formalin-embalmed human cadaver obtained from the body donor program of the Medical School, Australian National University. The donor had no known history of neuropathological disease. After removal of the dura mater, the brain was stored in 10% ethanol solution at room temperature for three years.
1. Preparation
<ol>
	<li>Obtain a whole brain from an embalmed human cadaver and remove the dura mater and store the brain in 10% ethanol at room temperature prior to dissection. 
	Caution: Use personal protection equipment in a well-ventilated room in accordance to local guidelines when handling. Ensure all participants are familiar with the institutional procedures for the safe handling and disposal of a scalpel and sharp objects before commencing the dissection protocol.</li>
	<li>Prepare the following instruments: scissors, forceps, scalpel blades (No. 15 and No. 22), metal probe, and the blunt end of a metal scalpel handle (Figure 1). Use the blunt end of the scalpel handle to minimise damage to the delicate nerve fibers and conserve the major white matter fiber tracts (Figure 2)13.</li>
	<li>Position the brain so that its ventral surface is facing upwards.</li>
</ol>
2. Dissection Procedure
NOTE: The dissection takes approximately 2 to 3 h to complete
<ol>
	<li>Remove the arachnoid mater and associated vasculature from both cerebral hemispheres using a pair of atraumatic (blunt) forceps.</li>
	<li>Gently lift the cerebellum and locate the inferior colliculi. Place the scalpel blade (No. 15) attached to a long scalpel handle just caudal to the inferior colliculi and cut axially through the brainstem. Keep the blade as close to horizontal as possible to avoid damaging the cerebellum. Take care to preserve the tectum of the midbrain.</li>
	<li>Position the brain to view the left or right lateral fissure. Starting at the supramarginal gyrus, use the blunt end of the scalpel handle to gently remove the superficial cortical layers. Gently move forward first above, then below the lateral sulcus to reveal the horizontal association fiber bundles running in the parietal, frontal, and temporal lobes, respectively.</li>
	<li>Follow the direction of the fibers arching around the posterior border of the insula connecting the superior and inferior longitudinal fasciculi to reveal the arcuate fasciculus.</li>
	<li>Anteriorly, gently remove the remaining superficial cortical layers of the middle temporal and inferior frontal gyri to reveal the uncinate fascicular fibers that connect the temporal and frontal lobes</li>
	<li>Identify the short gyri of the insular cortex and then remove the insula. Next remove the extreme capsule and claustrum to reveal the underlying external capsule. Note the bulge formed by the lentiform nucleus deep to the capsule. Moving towards the dorsal surface of the cortex, reveal the fibers of the corona radiata (Figure 4).</li>
	<li>Remove the remaining cortex and underlying white matter on the dorsal surface of the brain to reach the cingulate gyrus. Continue to use the blunt-end of the scalpel handle to remove the cingulate cortex to reveal the cingulum, the white matter tracts connecting the anterior perforated substance with the parahippocampal gyrus.</li>
	<li>Use the same technique to remove the cingulum from posterior to anterior to reveal the corpus callosum, composed of commissural fibers connecting the two cerebral hemispheres. The dorsum of the body (trunk) of the corpus callosum will now be visible (Figure 6).</li>
	<li>Repeat steps 2.3 to 2.8 on the contralateral cerebral hemisphere.</li>
	<li>Palpate and identify the extent of the lateral ventricle on one of the hemispheres. Using a probe, puncture the lateral wall of the ventricle at the site of the collateral trigone. Using a size 24 blade (attached to a No. 4 scalpel handle) enter through the puncture-site and cut inferiorly to open up the entire length of the inferior horn of the lateral ventricle.</li>
	<li>Now return to the ventricular collateral trigone to extend the cut superiorly towards the splenium of the corpus callosum (dotted line in Figure 5).</li>
	<li>Repeat steps 2.10 and 2.11 on the other hemisphere.</li>
	<li>Open the body of the lateral ventricle by continuing the incision from the trigone rostrally using a cut approximately 3 cm parallel to the corpus callosum in both hemispheres (dotted lines in Figure 6).</li>
	<li>Join the two parallel incisions in each hemisphere rostrally at the level of the genu and caudally at the level of the splenium of the corpus callosum. Using forceps, held in the non-dominant hand, gently lift the corpus callosum at the splenium. With a small sharp pair of scissors, held in the dominant hand, separate the splenium from the underlying septum pellucidum. Once you have reached the rostral end of the body, cut the corpus callosum and remove it.</li>
	<li>Nestle the ventral surface of the brain lengthwise on the palm of your non-dominant hand to stabilize the occipital and temporal areas (posterior part). At the same time, use your dominant hand to firmly but gently hold the anterior end of the brain by placing your opposed fingers and thumb on the lentiform nuclei of both sides of the brain.</li>
	<li>Using gentle pulling and twisting motions, physically separate the anterior and posterior parts of the brain taking special care to keep the choroid plexus intact. It is recommended that a colleague be present to guide the separation and gently section any remaining connecting tissues during the process using a scalpel.</li>
</ol>

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The authors declare that they have no conflict of interest.

The purpose of this paper was to devise a dissection guide for dissemination to teachers and students that could be used to enhance teaching and learning of the deep ventricular and periventricular structures of the human brain. We have devised a step-by-step guide with accompanying images, together with a video resource, that can be used to aid understanding of the morphology of the ventricles and their associated structures. The dissection technique itself is not new. Fiber dissection has been previously used for the s...

Many students struggle to comprehend the negative spaces of the ventricular system, located deep within the human brain1,2. Commonly used resources available for students to study the ventricles provide relatively crude representations of the intricate 3D relationships of these deep cerebral structures. Understanding the 3D anatomy of the ventricular system and related structures is particularly important in neurosurgery because access to the ventricular system is one of the most utilised techniques to measure intracranial pressure, decompress the ventricular system, and administer medications3. In addition, rapid advancements in medical imaging have necessitated the development of skills in the interpretation of 3D anatomy.
Two-dimensional (2D) sections of the brain in different planes are typically used to visualise the deep brain structures that form the boundaries of the negative ventricular spaces4. However, 2D slices of the brain alone are insufficient to enable students to understand the full extent of the 3D architecture of the ventricles and the fine details of the region such as fiber bundles connecting the cortex and subcortical structures5. Consequently, educators have to rely on the students&#39; own ability to compute a comprehensible 3D conception of the ventricles4. Students who struggle with spatial awareness find it extremely difficult to create this 3D image. Whilst plastic models and ventricular casts provide a 3D representation of the ventricular system, they fail to demonstrate the comprehensive relationships that form the boundaries of the ventricles. Students often mindlessly remove parts of the plastic model to access the ventricular system and understand its interconnections. In this process, they frequently overlook the detailed relative positions of each structure and lose understanding of their relationships (e.g.&#160;formation of the roof of the lateral ventricles by the corpus callosum).
The development of new computerised teaching tools has addressed some of these limitations. However, many of these models are limited to static text and images and do not take advantage of the interactivity offered by these new technologies7,8. Whilst interactive technologies enable the user to rotate 3D computer models to study multiple viewpoints, this can confuse some users especially novices who find it challenging to orientate structures6. Furthermore, interactive computer resources have been shown to be less effective in teaching more complex anatomical structures6. Thus, one of the challenges in neuroanatomy education is to provide students with resources that enable them to adequately visualize the ventricles and appreciate their 3D structure and anatomical relationships including the delicate associative, projection, and commissural fiber bundles that form complex relationships with the periventricular structures2.
Dissection has been shown to be an excellent educational method for learning anatomy7,8. A recent study provides evidence of the benefits of student dissection in learning neuroanatomy. In 2016, Rae et al. found improved short-term and long-term retention of neuroanatomy knowledge in students participating in dissections9. Whilst advances in technology continue to improve the accuracy and interactivity of 3D computer models, the knowledge acquired through hands-on dissection cannot be replicated digitally at the present time10.
In this study, we aimed to produce a reproducible dissection of a human brain. We chose a fiber dissection method because that allows preservation of the delicate fiber bundles and periventricular gray matter structures to better define the negative space of the ventricles.
Here we present a comprehensive step-by-step guide for creating a prosection model of the ventricles and periventricular structures together with an accompanying training video for use in neuroanatomy teaching and learning. These resources can be used for teaching and learning the neuroanatomy of the brain by both educators and students.

<table><tbody><tr><td>Scalpel Blade No 15</td><td>Swann-Morton</td><td>0205</td><td>Scalpel blade</td></tr><tr><td>Scalpel Blade No 11</td><td>Swann-Morton</td><td>0203</td><td>Scalpel blade</td></tr><tr><td>Scalpel Blade No 24</td><td>Swann-Morton</td><td>0211</td><td>Scalpel blade</td></tr><tr><td>Long Scalpel handle No3L</td><td>Swann-Morton</td><td>0913</td><td>Scalpel handle</td></tr><tr><td>Short Scalpel handle No4G</td><td>Swann-Morton</td><td>0934</td><td>Scalpel handle</td></tr><tr><td>Scissors</td><td></td><td></td><td>Scissors</td></tr><tr><td>Atraumatic Forceps</td><td></td><td></td><td>Atraumatic forceps</td></tr><tr><td>Toothed Forceps</td><td></td><td></td><td>Toothed forceps</td></tr><tr><td>Genelyn Arterial Enhanced</td><td>GMS Inovations</td><td>AE-475</td><td>Arterial embalming media</td></tr></tbody></table>

exploring deep space - uncovering the anatomy of periventricular structures to reveal the lateral ventricles of the human brain

Anatomy students are typically provided with two-dimensional (2D) sections and images when studying cerebral ventricular anatomy and students find this challenging. Because the ventricles are negative spaces located deep within the brain, the only way to understand their anatomy is by appreciating their boundaries formed by related structures. Looking at a 2D representation of these spaces, in any of the cardinal planes, will not enable visualisation of all of the structures that form the boundaries of the ventricles. Thus, using 2D sections alone requires students to compute their own mental image of the 3D ventricular spaces. The aim of this study was to develop a reproducible method for dissecting the human brain to create an educational resource to enhance student understanding of the intricate relationships between the ventricles and periventricular structures. To achieve this, we created a video resource that features a step-by-step guide using a fiber dissection method to reveal the lateral and third ventricles together with the closely related limbic system and basal ganglia structures. One of the advantages of this method is that it enables delineation of the white matter tracts that are difficult to distinguish using other dissection techniques. This video is accompanied by a written protocol that provides a systematic description of the process to aid in the reproduction of the brain dissection. This package offers a valuable anatomy teaching resource for educators and students alike. By following these instructions educators can create teaching resources and students can be guided to produce their own brain dissection as a hands-on practical activity. We recommend that this video guide be incorporated into neuroanatomy teaching to enhance student understanding of the morphology and clinical relevance of the ventricles.

This method of dissection exposes the ventricular system by separating the brain into an anterior and a posterior part (Figure 7 and Figure 8). The posterior part offers an internal view to the collateral trigone from which the posterior and inferior horns can be seen extending to the occipital and temporal lobes, respectively (Figure 8). In the inferior/temporal horn the hippocampus...

Watch this Scientific Journal Video about Exploring Deep Space - Uncovering the Anatomy of Periventricular Structures to Reveal the Lateral Ventricles of the Human Brain at JoVE.com

Exploring Deep Space - Uncovering the Anatomy of Periventricular Structures to Reveal the Lateral Ventricles of the Human Brain

This paper demonstrates the effective use of a fiber dissection method to reveal the superficial white matter tracts and periventricular structures of the human brain, in three-dimensional space, to aid student comprehension of ventricular morphology.

Anatomy students are typically provided with two-dimensional (2D) sections and images when studying cerebral ventricular anatomy and students find this ...

exploring-deep-space-uncovering-anatomy-periventricular-structures-to

Universidad de Cartagena UDEC

Research

JoVE Journal

Neuroscience

16.5K Views.  Australian National University. This paper demonstrates the effective use of a fiber dissection method to reveal the superficial white matter tracts and periventricular structures of the human brain, in three-dimensional space, to aid student comprehension of ventricular morphology.

Video: Exploring Deep Space - Uncovering the Anatomy of Periventricular Structures to Reveal the Lateral Ventricles of the Human Brain

The Subventricular Zone En-face: Wholemount Staining and Ependymal Flow

The walls of the lateral ventricles contain the largest germinal region in the adult mammalian brain. The subventricular zone (SVZ) in these walls is an extensively studied model system for understanding the behavior of neural stem cells and the regulation of adult neurogenesis. Traditionally, these studies have relied on classical sectioning techniques for histological analysis. Here we present an alternative approach, the wholemount technique, which provides a comprehensive, en-face view of this germinal region. Compared to sections, wholemounts preserve the complete cytoarchitecture and cellular relationships within the SVZ. This approach has recently revealed that the adult neural stem cells, or type B1 cells, are part of a mixed neuroepithelium with differentiated ependymal cells lining the lateral ventricles. In addition, this approach has been used to study the planar polarization of ependymal cells and the cerebrospinal fluid flow they generate in the ventricle. With recent evidence that adult neural stem cells are a heterogeneous population that is regionally specified, the wholemount approach will likely be an essential tool for understanding the organization and parcellation of this stem cell niche.

The lateral ventricle walls contain the largest germinal region in the adult mammalian brain. Traditionally, studies on neurogenesis in this region have relied on classical sectioning techniques for histological analysis. Here we present an alternative approach, the wholemount technique, which provides a comprehensive, en-face view of this germinal region.

The walls of the lateral ventricles contain the largest germinal region in the adult mammalian brain. The subventricular zone (SVZ) in these walls is an ...

A Visual Description of the Dissection of the Cerebral Surface Vasculature and Associated Meninges and the Choroid Plexus from Rat Brain

This video presentation was created to show a method of harvesting the two most important highly vascular structures, not residing within the brain proper, that support forebrain function. They are the cerebral surface (superficial) vasculature along with associated meninges (MAV) and the choroid plexus which are necessary for cerebral blood flow and cerebrospinal fluid (CSF) homeostasis. The tissue harvested is suitable for biochemical and physiological analysis, and the MAV has been shown to be sensitive to damage produced by amphetamine and hyperthermia 1,2. As well, the major and minor cerebral vasculatures harvested in MAV are of potentially high interest when investigating concussive types of head trauma. The MAV dissected in this presentation consists of the pial and some of the arachnoid membrane (less dura) of the meninges and the major and minor cerebral surface vasculature. The choroid plexus dissected is the structure that resides in the lateral ventricles as described by Oldfield and McKinley3,4,5,6. The methods used for harvesting these two tissues also facilitate the harvesting of regional cortical tissue devoid of meninges and larger cerebral surface vasculature, and is compatible with harvesting other brain tissues such as striatum, hypothalamus, hippocampus, etc. The dissection of the two tissues takes from 5 to 10 min total. The gene expression levels for the dissected MAV and choroid plexus, as shown and described in this presentation can be found at GSE23093 (MAV) and GSE29733 (choroid plexus) at the NCBI GEO repository. This data has been, and is being, used to help further understand the functioning of the MAV and choroid plexus and how neurotoxic events such as severe hyperthermia and AMPH adversely affect their function.

This video presentation shows a method of harvesting the two most important highly vascular structures that support forebrain function. They are the cerebral surface (superficial) vasculature along with associated meninges (MAV) and the choroid plexus which are necessary for cerebral blood flow and cerebrospinal fluid (CSF) homeostasis.

This video presentation was created to show a method of harvesting the two most important highly vascular structures, not residing within the brain ...

A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, hippocampus, and the associated parahippocampal regions (perirhinal, entorhinal,&#160;and parahippocampal proper). Unlike most other tracing protocols available, typically focusing on certain MTL areas (e.g., amygdala and/or hippocampus), the integrative perspective adopted by the present tracing guidelines allows for clear localization of all MTL subregions. By integrating information from a variety of sources, including extant tracing protocols separately targeting various MTL structures, histological reports, and brain atlases, and with the complement of illustrative visual materials, the present protocol provides an accurate, intuitive, and convenient guide for understanding the MTL anatomy. The need for such tracing guidelines is also emphasized by illustrating possible differences between automatic and manual segmentation protocols. This knowledge can be applied toward research involving not only structural MRI investigations but also structural-functional colocalization and fMRI signal extraction from anatomically defined ROIs, in healthy and clinical groups alike.

The present work provides a comprehensive set of guidelines for manually tracing the medial temporal lobe (MTL) structures. This protocol can be applied to research involving structural and/or combined structural-functional magnetic resonance imaging (MRI) investigations of the MTL, in both healthy and clinical groups.

The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, ...

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has been heavily studied. While many imaging studies treat the hippocampus as a single unitary neuroanatomical structure, it is, in fact, composed of several subfields that have a complex three-dimensional geometry. As such, it is known that these subfields perform specialized functions and are differentially affected through the course of different disease states. Magnetic resonance (MR) imaging can be used as a powerful tool to interrogate the morphology of the hippocampus and its subfields. Many groups use advanced imaging software and hardware (&#62;3T) to image the subfields; however this type of technology may not be readily available in most research and clinical imaging centers. To address this need, this manuscript provides a detailed step-by-step protocol for segmenting the full anterior-posterior length of the hippocampus and its subfields: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus (DG), strata radiatum/lacunosum/moleculare (SR/SL/SM), and subiculum. This protocol has been applied to five subjects (3F, 2M; age 29-57, avg. 37). Protocol reliability is assessed by resegmenting either the right or left hippocampus of each subject and computing the overlap using the Dice&#39;s kappa metric. Mean Dice&#39;s kappa (range) across the five subjects are: whole hippocampus, 0.91 (0.90-0.92); CA1, 0.78 (0.77-0.79); CA2/CA3, 0.64 (0.56-0.73); CA4/dentate gyrus, 0.83 (0.81-0.85); strata radiatum/lacunosum/moleculare, 0.71 (0.68-0.73); and subiculum 0.75 (0.72-0.78). The segmentation protocol presented here provides other laboratories with a reliable method to study the hippocampus and hippocampal subfields in vivo using commonly available MR tools.

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

The goal of this manuscript is to study the hippocampus and hippocampal subfields using MRI. The manuscript describes a protocol for segmenting the hippocampus and five hippocampal substructures: cornu ammonis (CA) 1, CA2/CA3, CA4/dentate gyrus, strata radiatum/lacunosum/moleculare, and subiculum.

The human hippocampus has been broadly studied in the context of memory and normal brain function and its role in different neuropsychiatric disorders has ...

3D Modeling of the Lateral Ventricles and Histological Characterization of Periventricular Tissue in Humans and Mouse

The ventricular system carries and circulates cerebral spinal fluid (CSF) and facilitates clearance of solutes and toxins from the brain. The functional units of the ventricles are ciliated epithelial cells termed ependymal cells, which line the ventricles and through ciliary action are capable of generating laminar flow of CSF at the ventricle surface. This monolayer of ependymal cells also provides barrier and filtration functions that promote exchange between brain interstitial fluids (ISF) and circulating CSF. Biochemical changes in the brain are thereby reflected in the composition of the CSF and destruction of the ependyma can disrupt the delicate balance of CSF and ISF exchange. In humans there is a strong correlation between lateral ventricle expansion and aging. Age-associated ventriculomegaly can occur even in the absence of dementia or obstruction of CSF flow. The exact cause and progression of ventriculomegaly is often unknown; however, enlarged ventricles can show regional and, often, extensive loss of ependymal cell coverage with ventricle surface astrogliosis and associated periventricular edema replacing the functional ependymal cell monolayer. Using MRI scans together with postmortem human brain tissue, we describe how to prepare, image and compile 3D renderings of lateral ventricle volumes, calculate lateral ventricle volumes, and characterize periventricular tissue through immunohistochemical analysis of en face lateral ventricle wall tissue preparations. Corresponding analyses of mouse brain tissue are also presented supporting the use of mouse models as a means to evaluate changes to the lateral ventricles and periventricular tissue found in human aging and disease. Together, these protocols allow investigations into the cause and effect of ventriculomegaly and highlight techniques to study ventricular system health and its important barrier and filtration functions within the brain.

Using MRI scans (human), 3D imaging software, and immunohistological analysis, we document changes to the brain&#8217;s lateral ventricles. Longitudinal 3D mapping of lateral ventricle volume changes and characterization of periventricular cellular changes that occur in the human brain due to aging or disease are then modeled in mice.

The ventricular system carries and circulates cerebral spinal fluid (CSF) and facilitates clearance of solutes and toxins from the brain. The functional ...

High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem

The focus of this study was to test the resolution limits of structural MRI of a postmortem brain compared to living human brains. The resolution of structural MRI in vivo is ultimately limited by physiological noise, including pulsation, respiration and head movement. Although imaging hardware continues to improve, it is still difficult to resolve structures on the millimeter scale. For example, the primary visual sensory pathways synapse at the lateral geniculate nucleus (LGN), a visual relay and control nucleus in the thalamus that normally is organized into six interleaved monocular layers. Neuroimaging studies have not been able to reliably distinguish these layers due their small size that are less than 1 mm thick.
The resolving limit of structural MRI, in a postmortem brain was tested using multiple images averaged over a long duration (~24 h). The purpose was to test whether it was possible to resolve the individual layers of the LGN in the absence of physiological noise. A proton density (PD)1 weighted pulse sequence was used with varying resolution and other parameters to determine the minimum number of images necessary to be registered and averaged to reliably distinguish the LGN and other subcortical regions. The results were also compared to images acquired in living human brains. In vivo subjects were scanned in order to determine the additional effects of physiological noise on the minimum number of PD scans needed to differentiate subcortical structures, useful in clinical applications.

High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem

Here we present a protocol to determine the minimum number images that needed to be registered and averaged to resolve subcortical structures and test whether the individual layers of the LGN could be resolved in the absence of physiological noise.

The focus of this study was to test the resolution limits of structural MRI of a postmortem brain compared to living human brains. The resolution of ...

Microdissection of Mouse Brain into Functionally and Anatomically Different Regions

The brain is the command center for the mammalian nervous system and an organ with enormous structural complexity. Protected within the skull, the brain consists of an outer covering of grey matter over the hemispheres known as the cerebral cortex. Underneath this layer reside many other specialized structures that are essential for multiple phenomenon important for existence. Acquiring samples of specific gross brain regions requires quick and precise dissection steps.&#160;It is understood that at the microscopic level, many sub-regions exist and likely cross the arbitrary regional boundaries that we impose for the purpose of this dissection.
Mouse models are routinely used to study human brain functions and diseases. Changes in gene expression patterns may be confined to specific brain areas targeting a particular phenotype depending on the diseased state. Thus, it is of great importance to study regulation of transcription with respect to its well-defined structural organization. A complete understanding of the brain requires studying distinct brain regions, defining connections, and identifying key differences in the activities of each of these brain regions. A more comprehensive understanding of each of these distinct regions may pave the way for new and improved treatments in the field of neuroscience. Herein, we discuss a step-by-step methodology for dissecting the mouse brain into sixteen distinct regions. In this procedure, we have focused on male mouse C57Bl/6J (6-8 week old) brain removal and dissection into multiple regions using neuroanatomical landmarks to identify and sample discrete functionally-relevant and behaviorally-relevant&#160;brain regions. This work will help lay a strong foundation in the field of neuroscience, leading to more focused approaches in the deeper understanding of brain function.

We present a hands-on, step-by-step, rapid protocol for mouse brain removal and dissection of discrete regions from fresh brain tissue. Obtaining brain regions for molecular analysis has become routine in many neuroscience labs. These brain regions are immediately frozen to obtain high quality transcriptomic data for system level analysis.

The brain is the command center for the mammalian nervous system and an organ with enormous structural complexity. Protected within the skull, the brain ...

A Standardized Pipeline for Examining Human Cerebellar Grey Matter Morphometry using Structural Magnetic Resonance Imaging

Multiple lines of research provide compelling evidence for a role of the cerebellum in a wide array of cognitive and affective functions, going far beyond its historical association with motor control. Structural and functional neuroimaging studies have further refined understanding of the functional neuroanatomy of the cerebellum beyond its anatomical divisions, highlighting the need for the examination of individual cerebellar subunits in healthy variability and neurological diseases. This paper presents a standardized pipeline for examining cerebellum grey matter morphometry that combines high-resolution, state-of-the-art approaches for optimized and automated cerebellum parcellation (Automatic Cerebellum Anatomical Parcellation using U-Net Locally Constrained Optimization; ACAPULCO) and voxel-based registration of the cerebellum (Spatially Unbiased Infra-tentorial Template; SUIT) for volumetric quantification. 
The pipeline has broad applicability to a range of neurological diseases and is fully automated, with manual intervention only required for quality control of the outputs. The pipeline is freely available, with substantial accompanying documentation, and can be run on Mac, Windows, and Linux operating systems. The pipeline is applied in a cohort of individuals with Friedreich ataxia (FRDA), and representative results, as well as recommendations on group-level inferential statistical analyses, are provided. This pipeline could facilitate reliability and reproducibility across the field, ultimately providing a powerful methodological approach for characterizing and tracking cerebellar structural changes in neurological diseases.

A standardized pipeline is presented for examining cerebellum grey matter morphometry. The pipeline combines high-resolution, state-of-the-art approaches for optimized and automated cerebellum parcellation and voxel-based registration of the cerebellum for volumetric quantification.

Multiple lines of research provide compelling evidence for a role of the cerebellum in a wide array of cognitive and affective functions, going far beyond ...

Visualization of Brain Pericyte Contractility Post-Subarachnoid Hemorrhage

Imaging Vital and Non-vital Brain Pericytes in Brain Slices following Subarachnoid Hemorrhage

Pericytes are crucial mural cells situated within cerebral microcirculation, pivotal in actively modulating cerebral blood flow via contractility adjustments. Conventionally, their contractility is gauged by observing morphological shifts and nearby capillary diameter changes under specific circumstances. Yet, post-tissue fixation, evaluating vitality and ensuing pericyte contractility of imaged brain pericytes becomes compromised. Similarly, genetically labeling brain pericytes falls short in distinguishing between viable and non-viable pericytes, particularly in neurologic conditions like subarachnoid hemorrhage (SAH), where our preliminary investigation validates brain pericyte demise. A reliable protocol has been devised to surmount these constraints, enabling simultaneous fluorescent tagging of both functional and non-functional brain pericytes in brain sections. This labeling method allows high-resolution confocal microscope visualization, concurrently marking the brain slice microvasculature. This innovative protocol offers a means to appraise brain pericyte contractility, its impact on capillary diameter, and pericyte structure. Investigating brain pericyte contractility within the SAH context yields insightful comprehension of its effects on cerebral microcirculation.

Author Spotlight: Imaging Pericytes Post-Subarachnoid Hemorrhaging in Rodents 

The preliminary inquiry confirms that subarachnoid hemorrhage (SAH) causes brain pericyte demise. Evaluating pericyte contractility post-SAH requires differentiation between viable and non-viable brain pericytes. Hence, a procedure has been developed to label viable and non-viable brain pericytes concurrently in brain sections, facilitating observation using a high-resolution confocal microscope.

Pericytes are crucial mural cells situated within cerebral microcirculation, pivotal in actively modulating cerebral blood flow via contractility ...

Enhancing Neuroimaging Analysis in Brain Disorders

Manual Segmentation of the Human Choroid Plexus Using Brain MRI

The choroid plexus has been implicated in neurodevelopment and a range of brain disorders. Evidence demonstrates that the choroid plexus is critical for brain maturation, immune/ inflammatory regulation, and behavioral/cognitive functioning. However, current automated neuroimaging segmentation tools are poor at accurately and reliably segmenting the lateral ventricle choroid plexus. Furthermore, there is no existing tool that segments the choroid plexus located in the third and fourth ventricles of the brain. Thus, a protocol delineating how to segment the choroid plexus in the lateral, third, and fourth ventricle is needed to increase the reliability and replicability of studies examining the choroid plexus in neurodevelopmental and brain disorders. This protocol provides detailed steps to create separately labeled files in 3D Slicer for the choroid plexus based on DICOM or NIFTI images. The choroid plexus will be manually segmented using the axial, sagittal, and coronal planes of T1w images making sure to exclude voxels from gray or white matter structures bordering the ventricles. Windowing will be adjusted to assist in the localization of the choroid plexus and its anatomical boundaries. Methods for assessing accuracy and reliability will be demonstrated as part of this protocol. Gold standard segmentation of the choroid plexus using manual delineations can be used to develop better and more reliable automated segmentation tools that can be openly shared to elucidate changes in the choroid plexus across the lifespan and within various brain disorders.

Author Spotlight: Bridging Gaps in Anatomy and Establishing a Foundation for Algorithmic Studies 

Despite the crucial role of the choroid plexus in the brain, neuroimaging studies of this structure are scarce due to the lack of reliable automated segmentation tools. The present protocol aims to ensure gold-standard manual segmentation of the choroid plexus that can inform future neuroimaging studies.

The choroid plexus has been implicated in neurodevelopment and a range of brain disorders. Evidence demonstrates that the choroid plexus is critical for ...

Exploring Deep Space - Uncovering the Anatomy of Periventricular Structures to Reveal the Lateral Ventricles of the Human Brain

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Chapters in this video

The Subventricular Zone En-face: Wholemount Staining and Ependymal Flow

A Visual Description of the Dissection of the Cerebral Surface Vasculature and Associated Meninges and the Choroid Plexus from Rat Brain

A Comprehensive Protocol for Manual Segmentation of the Medial Temporal Lobe Structures

High-resolution In Vivo Manual Segmentation Protocol for Human Hippocampal Subfields Using 3T Magnetic Resonance Imaging

3D Modeling of the Lateral Ventricles and Histological Characterization of Periventricular Tissue in Humans and Mouse

High-resolution Structural Magnetic Resonance Imaging of the Human Subcortex In Vivo and Postmortem

Microdissection of Mouse Brain into Functionally and Anatomically Different Regions

A Standardized Pipeline for Examining Human Cerebellar Grey Matter Morphometry using Structural Magnetic Resonance Imaging

Imaging Vital and Non-vital Brain Pericytes in Brain Slices following Subarachnoid Hemorrhage

Manual Segmentation of the Human Choroid Plexus Using Brain MRI