Name: utilizing 3d printing technology to merge mri with histology: a protocol for brain sectioning
Uploaded: 2016-12-06T13:00:00.000+00:00
Duration: 15 min 53 s
Description: Watch this Scientific Journal Video about Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning at JoVE.com

The Intramural Research Program of NINDS supported this study. We thank the NIH Functional Magnetic Resonance Imaging Facility. We thank Jennifer Lefeuvre and Cecil Chern-Chyi Yen for assistance with postmortem MRI acquisition. We thank John Ostuni and the Section on Instrumentation Core Facility for assistance with 3D printing. Figure 1 of this work used snapshots from MeshLab, a tool developed with the support of the 3D-CoForm project.

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The authors declare that they have no competing financial interests.

여기에 설명 된 프로토콜은 MRI 및 조직학 섹션 사이의 정확한 비교를 할 수 있습니다. 프로토콜은 이러한 마모 셋 또는 설치류 사람이나 작은 동물의 뇌에 적용 할 수있는 통합 된 형식으로 제공된다. 대형 (인간)에 대한 구체적이고 두뇌가 강조된다 (인간이 아닌 영장류와 설치류) 작은 및 첨부 된 비디오와 그림의 차이는 우리는 비단 원숭이에서 응용 프로그램을 보여줍니다. 접근 방법은 간단하지만,이 방법은 여러 단계뿐만 아니라 여러 종류의 소프트웨어의 사용을 요구한다. 또한, 잠재적으로이 방법의 정확도에 영향을주는 여러 가지 문제를 언급하는 것이 중요하다. 생체 MRI의 화질은 중요한 인자이다. MRI 디지털화 조직학 이미지 간의 이미지 해상도에서의 차이를 최소화하기 위해 가능한 한 작은 MRI 복셀의 크기가 사용되어야한다. 이 개념은 또한 사후 MRI의 화질에 적용된다. 증가하는 동안사후 MRI에서의 획득 시간이 제제는 기포 관련된 초점 신호 끊김 같은 이미지 아티팩트들을 도입 할 수있다, 더 높은 이미지 해상도를 허용한다. 이러한 아티팩트는 조직 영역을 모호뿐만 아니라 형상에 영향을 미칠 수있다. 또한, 사후 MRI에서 조직의 크기는 정착 과정 및 시간에 의해 영향을받을 가능성이 높다. 생체 내 생체 MRI 경기에 밀접 취득 중에 조각 형상 설정의 해부학 적 구조를 이용하여 근사화 될 수 있지만, 비선형 등록이 여전히 두 MRI 이미지 매칭 정밀도 높은 수준에 도달 할 필요가있을 것이다. 뇌 홀더와 슬라이서의 설계는 중요한 단계이다. 뇌의 디지털 모델을 만들 때, 평활 알고리즘은 다소 고정 뇌 모델 상대를 확대하는 것이 적용된다. 이 홀더 및 슬라이서로 뇌를 쉽게 삽입 할 수 있습니다 홀더에 날카로운 모서리를 줄여 &amp;# 39;의 윤곽. 모델이 너무 클 경우 (예 : 5 % 이상), 뇌 MRI는 사후 및 / 또는 단면 동안 이동할 수있다. 또 다른 중요한 점은 소뇌 제대로 인쇄 3D 객체 내부에 배치되도록 뇌 모델의 설계를 적용하는 것이다. 소뇌가 부검 뇌에서 추출 중에 손상된 경우가 특히 어려울 수있다. 뇌 슬라이서 홀더를 인쇄 할 때, 3 차원 프린터 유형은 신중하게 선택되어야한다. 일부 다중 - 제트 프린터는 지지체 물질을 제거하기 위해 오븐을 이용하여 후 처리를 필요로한다. 이 프린터는 방수 및 데스크톱 융합 증착 모델링 (FDM) 프린터보다 상대적으로 내구성이 객체를 생성 할 수 있지만, 가열 공정은 뇌의 윤곽에 완벽하게 수직하지 않은 블레이드 격차를 작성, 약간 상자를 워프 할 수 있습니다 지원을 제거합니다. 뇌 절편 과정은 또 다른 중요한 단계입니다. 일을 절단하기 전에전자 석판으로 전체 뇌, 뇌가 뇌 슬라이서 내부에 단단하게 앉아 있는지 확인하는 것이 중요하다 : 약간의 압력이 뇌에 적용되는 어떤 움직임이 없어야합니다. 이로써 블레이드 연구자에 의해 설정된 위치에서 정확하게 뇌을 극복 할 수 있도록한다. 절단시 연속, 균형 잡힌 압력이 모두 블레이드 홀더 적용해야합니다. 블레이드의 선명도 및 조직의 강성에 따라 약간의 횡 절단 동작 평면 절단면을 유지하는데 바람직 할 수있다. 파라핀 매립 공정은 MRI 및 조직학 간의 오정렬의 원인이 될 수있다. 티슈 슬래브 매립 과정 카세트에 평평 앉아 있지 않으면, 마이크로톰의 절단면 및 슬래브의 표면 위치 사이의 기울기가있을 것이다. 이것은 모든 조직이 노출 된 평면을 찾을 수 없게 부분 절단이 필요하다. 틸트를 보정하는 한 가지 방법높은 등방성 해상도 사후의 MRI에서 보는면의 각도를 변경하는 것이다. 그러나, 이것은 일반적으로 이방성 해상도 (일반적으로 관상 슬라이스 두께)로 취득한 생체 MRI에서 수행하는 것은 거의 불가능하다. 마지막으로, 조직뿐만 아니라 (주름, 균열, 접이식) 슬라이드의 제조 동안 포르말린 고정 파라핀 기간 임베딩 (수축) 중 일부의 변형이 발생할 수있다. 이러한 변형 중 일부는 슬라이드 상에 전송하기 전에 수욕에서 4-5 ㎛의 섹션을 바꾸어 보정 될 수있다. 다른 변형 부분적 사후 MRI 이미지 조직학 디지털화 된 이미지의 변형 화상 coregistration를 수행함으로써 해결 될 수있다. 그럼에도 불구하고, 신중하고 숙련 된 연습과 변형을 최소화하는 섹션을 조직학하기 위해 MRI 볼륨을 일치에 가장 효과적인 방법이다. 결론적으로, 여기에 소개 된 방법은 INV 수 있습니다estigators 정확하게 MRI 소견의 기본 병리를 평가합니다. 보다 일반적으로, 그것은 식별 및 / 또는 염증이나 재유 수화와 같은 특정 병리학 적 프로세스를 대상으로 조사 연구를위한 새로운 MRI 바이오 마커를 검증하기위한 유망한 방법이다.

In vivo MRI provides a noninvasive and sensitive measure of tissue integrity at the macroscopic level. Changes in MRI signal intensity seen in vivo are outcome measures in many ongoing clinical trials.1 While the intensity changes seen via MRI can identify areas of abnormality in the context of the whole brain, they are often not sufficiently specific to differentiate pathological processes. This is especially true of dynamic processes involving multiple pathologies. For example, in multiple sclerosis (MS) or its animal model, experimental autoimmune encephalomyelitis (EAE), inflammation, edema, myelin degradation, axonal destruction, gliosis, and neuronal death overlap. 2, 3 To obtain the necessary specificity regarding the underlying pathology, context must be taken into account, together with knowledge of the histology of the MRI-identified abnormal tissues.
However, even in well-controlled animal experiments, matching histology with in vivo MRI is fundamentally challenging for various reasons. First, the difference in dimensional scales between histology sections and MRI is of several orders of magnitude.4 Second, for proper comparison, the orientation of MRI slice plane must match the sectioning plane of the brain tissue when cut. Due to the shape of the brain, it is very difficult to make consistently straight and accurate cuts when the brain is sitting on a flat surface. Third, the large size of the brain relative to a potentially small area of interest (lesion, tumor, etc.) creates a "needle-in-a-haystack" scenario for the pathologist processing the tissue. Fourth, even when the target tissue is found, it is commonly processed in such a way as to render virtually impossible an association with the original MRI data. Finally, traditional pathological sectioning of brain tissue is often imprecise and inconsistent, further complicating the comparison between histology sections and MRI images. 
 Previous attempts to overcome these challenges relied on the use of deformational algorithms to coregister the data and/or placement of fiducial markers within or around the tissue as a reference.5, 6, 7, 8 The former approach requires complex computational models that are particularly susceptible to complications due to data formatting, imaging artifacts, and changes caused by tissue processing.4 On the other hand, the latter approach introduces the possibility of contaminating or otherwise harming the tissue itself.9
The approach described here improves the transition between modalities through the use of postmortem MRI to bridge the gap between in vivo MRI and histology. Postmortem MRI provides three-dimensional (3D) images of the brain at higher resolution than can be achieved in vivo and furthermore provides the data needed for producing a morphologically accurate model of the brain surface. This digital model can then be used to create a 3D-printed custom holder for the brain. With careful positioning, the brain holder allows for precise, MRI-oriented brain sectioning, reducing the need for complex mathematical algorithms, and enables a focus on specific regions for targeted sampling. 
Our laboratory recently introduced new methods for creating custom brain holders and slicers using postmortem MRI and 3D-printing technology for human10 and marmoset brains.4 The two methods allow for a more accurate correlation between MRI and histology in a research setting, and ultimately allow a deeper understanding of the specific pathology underlying MRI abnormalities. Carefully designed experiments, in which the brain is sampled repeatedly over time in vivo, can provide context for interpretation of the pathology, which in turn can add specificity to interpretation of the MRI. Here, we present a modified protocol in a unified framework that can be applied to any brain tissue, whether it derive from nonhuman primates, rodents, or humans. We provide detailed instructions, and a corresponding video, for the marmoset sectioning. Although the overall protocol applies to any type of brain, due to differences in MRI acquisition and tissue size, as well as the challenges encountered when dealing with specific brain types, there are some differences in the approach depending on the type of brain being processed. In this presentation, sections with "human" will denote differences in protocol specific to the human brain.

<table><tbody><tr><td>7T/30cm USR AVIII Bruker MRI</td><td>Bruker Biospin</td><td></td><td></td></tr><tr><td>38 mm Bruker Biospin volume coil</td><td>Bruker Biospin</td><td></td><td></td></tr><tr><td>Fomblin</td><td>Solvay Solexis</td><td></td><td></td></tr><tr><td>50 ml Falcon Centrifuge Tubes, Polypropylene, Sterile</td><td>Corning</td><td>21008-951</td><td></td></tr><tr><td>Fisherbrand Gauze Sponges</td><td>Fisher Scientrific</td><td>13-761-52</td><td></td></tr><tr><td>Parafilm M All-Purpose Laboratory Film</td><td>Bemis</td><td></td><td></td></tr><tr><td>Leica RM2235 rotary microtome&amp;nbsp;</td><td>Leica</td><td></td><td></td></tr><tr><td>Leica Disposable Blades, low profile (819)</td><td>Leica</td><td></td><td></td></tr><tr><td>Cresyl Violet Acetate, 0.1% Aqueous</td><td>Electron Microscopy Sciences</td><td>26089-01</td><td></td></tr><tr><td>Luxol Fast Blue, 0.1% in 95% Alcohol</td><td>Electron Microscopy Sciences</td><td>26056-15</td><td></td></tr><tr><td>ETOH</td><td></td><td></td><td></td></tr><tr><td>Ultimaker 2 Extended&amp;nbsp;</td><td>Ultimaker</td><td></td><td></td></tr><tr><td>.75 kg Official Ultimaker Branded PLA&amp;nbsp; Filament, 2.85 mm, Silver Metallic</td><td>Ultimaker</td><td></td><td></td></tr><tr><td>Axio Observer.Z1</td><td>Zeiss</td><td></td><td></td></tr><tr><td>Zen 2 (Blue Edition)</td><td>Zeiss</td><td></td><td></td></tr><tr><td>Netfabb Professional 5.0.1</td><td>Netfabb</td><td>http://www.netfabb.com/professional.php</td><td></td></tr><tr><td>Meshmixer 10.9.332</td><td>Autodesk</td><td>http://www.meshmixer.com/download.html</td><td></td></tr><tr><td>Mipav 7.2</td><td>NIH CIT</td><td>http://mipav.cit.nih.edu</td><td></td></tr><tr><td>Cura</td><td>Ultimaker</td><td>https://ultimaker.com/en/products/cura-software</td><td></td></tr></tbody></table>

utilizing 3d printing technology to merge mri with histology: a protocol for brain sectioning

Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume three-dimensionally. While MRI is an extremely sensitive tool for detecting tissue abnormalities, association of signal changes with an underlying pathological process is usually not straightforward. In the central nervous system, for example, inflammation, demyelination, axonal damage, gliosis, and neuronal death may all induce similar findings on MRI. As such, interpretation of MRI scans depends on the context, and radiological-histopathological correlation is therefore of the utmost importance. Unfortunately, traditional pathological sectioning of brain tissue is often imprecise and inconsistent, thus complicating the comparison between histology sections and MRI. This article presents novel methodology for accurately sectioning primate brain tissues and thus allowing precise matching between histology and MRI. The detailed protocol described in this article will assist investigators in applying this method, which relies on the creation of 3D printed brain slicers. Slightly modified, it can be easily implemented for brains of other species, including humans.

이 방법의 흐름은 뇌가 분리되면, 슬래브의 표면면의 MR 이미지 및 이미지와 시각적으로 비교하여 여러 석판 걸쳐 양호한 방향이 일치 (도 2)을 나타낸다도 1에 요약 하였다. 슬래브는 파라핀에 포함 된 후, 그들은 마이크로톰에 절단 및 스테인드된다. 높은 해상도 사후 MRI와 스테인드 조직학 섹션 사이의보다 철저한 비교는 비단 원숭이 뇌의 모든 구조에서 정확하고 일관된 경기 (그림 3)를 보여줍니다. MS이 동물 모델에서, 동물 뇌 백색질 퍼져 백질 병변을 개발한다. 이러한 병변은 MRI를 수행하여 비 침습적으로 검출 할 수있다. 도 4는 MRI 소견 병리학 기판 해명이 기술의 능력을 보여준다. 생체 내 MRI에서 발견 된 작은 병변 수사후 MRI 및 조직학 모두 추적 할 수. 인 세트에 도시 된 바와 같이, 병변 내 탈수 초화는 (주변 조직에 비해 hyperintensity)이 MR 신호 변화를 주도 주요 구성 요소 중 하나이다. 조직학 및 사후 MRI는 생체 내 MRI (그림 4)에서 놓친 병변을 표시 할 수 있습니다. <img alt="그림 1" src="/files/ftp_upload/54780/54780fig1.jpg" /> 비단 원숭이의 뇌 슬라이서 상자를 만드는 1. 워크 플로우 그림. 뇌는 포르말린 (A1)과 T2 강조 MRI는 에지 당 150 μm의 (A2)의 등방성 복셀로 취득으로 고정되어있다. 이미지 처리 및 바이너리 마스크 (A3)을 만들 임계 된 있습니다. 표면이어서 3D 모델링 소프트웨어 (A4)에 렌더링된다. 슬라이서 템플릿과 뇌 모델 사이의 부울 뺄셈은 뇌 슬라이서 (B1)의 디지털 모델을 생성합니다. 뇌 슬라이서 상자는 3D 프린터 (B2)에 인쇄되어 있습니다. 뇌는 다음 슬라이서 상자에 단단히 배치절단 (B3). <a href="https://ecsource-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/54780fig1large.jpg" target="_blank">이 그림의 더 큰 버전을 보려면 여기를 클릭하십시오.</a> <img alt="그림 2" src="/files/ftp_upload/54780/54780fig2.jpg" /> 그림 2.에서 왼쪽에서 오른쪽으로 : 생체 내 MRI, 사후 MRI, 조직 슬래브 사진. 슬라이싱 평면은 대응하는 생체 MRI 슬라이스 (A)에 비해 시각적 사후 MRI (B)에 기초하여 설정 하였다. 뇌 후 절단하고, 얻어진 슬래브 일관성 (C) 인 것으로 밝혀졌다. <a href="https://ecsource-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/54780fig2large.jpg" target="_blank">이 그림의 더 큰 버전을 보려면 여기를 클릭하십시오.</a> <img alt="그림 3" src="/files/ftp_upload/54780/54780fig3.jpg" /> 그림 3. 고해상도 사후의 MRI 및 조직학부분 일치. 슬래브는 4 μm의 섹션으로 마이크로톰 절단, 빠른 파란색과 크레 실 바이올렛 (B)로 염색, 파라핀에 포함되었다. 섹션은 다음 시각적으로 100 μm의의 T2 * 뇌 구조 (A)에 따라 MRI -weighted와 일치 하였다. 이 이미지를 획득하기위한 세부 사항은 프로토콜 및 표 1. 뇌 구조의 보조 섹션에서 : (1) 빨간색 화살표 = 내부 캡슐, 파란색 화살표 = 전방 접합면; (2) 빨간색 화살표 = 피질, 파란색 화살표 = 광학 기관; (3) 빨간색 화살표 = 미상, 파란색 화살표 = 해마; (4) 빨간색 화살표 = 뇌량, 파란색 화살표 = 대뇌 말라; (5) 빨간색 화살표 = 열등 둔덕, 파란색 화살표 = 피라미드 기관. B1의 점선 박스는 하나의 뇌 절단 또는 파라핀 매립 중에 에러가 좌측 전방 접합면의 불일치로 이어지는 상기 Y 축을 중심으로 약간 회전 의한 슬라이스를 나타낸다. <a href="https://ecsource-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/54780fig3large.jpg" target="_blank">을 보려면 여기를 클릭하십시오</a>이 그림의 더 큰 버전. <img alt="그림 4" src="/files/ftp_upload/54780/54780fig4.jpg" /> 그림 4. 조직 학적 섹션으로 생체 내 MRI에서 병변을 추적. 생체 내 MRI 중 하나 광학 기관 (A1)의 병변을 제안하는 이상 hyperintensity 신호의 더 설득력있는 증거가 없었다. 그러나, 높은 해상도 사후의 MRI는 모두 광학 책자 (A2)의 명확한 하이퍼 강렬한 라인을 보여줍니다. 4 μm의 조직 학적 섹션의 빠른 블루 / 크레 실 바이올렛 얼룩은 생체 MRI에 본 hyperintense의 영역 (A3)을 탈수 초 것을 보여줍니다. 대뇌 백질에서, 생체 내 MRI 미묘한 양자 hyperintensity (B1, 인 세트의 확대)를 보여줍니다. hyperintense 지역은 높은 해상도 사후 MRI (B2)에 대한 명백하다. 4 μm의 조직 학적 섹션의 LFB 염색이 영역 (B3)를 탈수 초 것을 보여줍니다. 기준 I와 비교 한 후N 생체 MRI 및 hemotoxylin - 및 - 에오신 염색, 우측은 해부학 적 이상이 아닌 탈수 초 병변 인 것으로 측정되었다. <a href="https://ecsource-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/54780fig4large.jpg" target="_blank">이 그림의 더 큰 버전을 보려면 여기를 클릭하십시오.</a> <img alt="기업 코드 파일" src="/files/ftp_upload/54780/54780supplementalfiles.jpg" /> 기업 코드 파일. Brain_Slicer_Parts_Marmoset.stl : <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/Brain_Slicer_Parts_Marmoset.stl" target="_blank">이 파일을 다운로드하려면 여기를 클릭하십시오.</a> Brain_Slicer_Parts_Human.stl : <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/Brain_Slicer_Parts_Human.stl" target="_blank">이 파일을 다운로드하려면 여기를 클릭하십시오.</a> Cap_Insert.stl : <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54780/Cap_Insert.stl" target="_blank">이 파일을 다운로드하려면 여기를 클릭하십시오.</a>

Watch this Scientific Journal Video about Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning at JoVE.com

Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning

이 프로토콜의 전반적인 목적은 정확하게 정의 된 3D 인쇄 뇌 홀더 및 슬라이서 박스의 생성을 통해 조직학 섹션 자기 공명 영상 (MRI) 이미지 볼륨을 정렬하는 것이다.

3D 인쇄 기술을 활용하여 조직학과 MRI를 병합하기 : 두뇌를위한 프로토콜 단면

Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume ...

utilizing-3d-printing-technology-to-merge-mri-with-histology-protocol

Universidad San Sebastian

Research

JoVE Journal

Neuroscience

14.8K 조회수.  National Institute of Neurological Disorders and Stroke.  이 프로토콜의 전반적인 목적은 정확하게 정의 된 3D 인쇄 뇌 홀더 및 슬라이서 박스의 생성을 통해 조직학 섹션 자기 공명 영상 (MRI) 이미지 볼륨을 정렬하는 것이다. 

비디오: Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning

Registered Bioimaging of Nanomaterials for Diagnostic and Therapeutic Monitoring 

Nanomedications can be carried by blood borne monocyte-macrophages into the reticuloendothelial system (RES; spleen, liver, lymph nodes) and to end organs. The latter include the lung, RES, and brain and are operative during human immunodeficiency virus type one (HIV-1) infection. Macrophage entry into tissues is notable in areas of active HIV-1 replication and sites of inflammation. In order to assess the potential of macrophages as nanocarriers, superparamagnetic iron-oxide and/or drug laden particles coated with surfactants were parenterally injected into HIV-1 encephalitic mice. This was done to quantitatively assess particle and drug biodistribution. Magnetic resonance imaging (MRI) test results were validated by histological coregistration and enhanced image processing. End organ disease as typified by altered brain histology were assessed by MRI. The demonstration of robust migration of nanoformulations into areas of focal encephalitis provides '"proof of concept" for the use of advanced bioimaging techniques to monitor macrophage migration. Importantly, histopathological aberrations in brain correlate with bioimaging parameters making the general utility of MRI in studies of cell distribution in disease feasible. We posit that using such methods can provide a real time index of disease burden and therapeutic efficacy with translational potential to humans.

Registered Bioimaging of Nanomaterials for Diagnostic and Therapeutic Monitoring

Bioimaging methods used to assess cell biodistribution of nanoparticles are applicable for therapeutic and diagnostic monitoring of nanoformulated compounds. The methods described herein are sensitive and specific when assessed by histological coregistration. The methodologies provide a translational pathway from rodent to human applications.

진단 및 치료 모니터링을위한 Nanomaterials 등록 Bioimaging

Nanomedications can be carried by blood borne monocyte-macrophages into the reticuloendothelial system (RES; spleen, liver, lymph nodes) and to end ...

연구

생체공학

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.

인간과 마우스의 뇌실 주위 조직의 측면 심실 및 조직 학적 특성의 3D 모델링

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

신경과학

A MRI-Based Toolbox for Neurosurgical Planning in Nonhuman Primates

In this paper, we outline a method for surgical preparation that allows for the practical planning of a variety of neurosurgeries in NHPs solely using data extracted from magnetic resonance imaging (MRI). This protocol allows for the generation of 3D printed anatomically accurate physical models of the brain and skull, as well as an agarose gel model of the brain modeling some of the mechanical properties of the brain. These models can be extracted from MRI using brain extraction software for the model of the brain, and custom code for the model of the skull. The preparation protocol takes advantage of state-of-the-art 3D printing technology to make interfacing brains, skulls, and molds for gel brain models. The skull and brain models can be used to visualize brain tissue inside the skull with the addition of a craniotomy in the custom code, allowing for better preparation for surgeries directly involving the brain. The applications of these methods are designed for surgeries involved in neurological stimulation and recording as well as injection, but the versatility of the system allows for future expansion of the protocol, extraction techniques, and models to a wider scope of surgeries.

The method outlined below aims to provide a comprehensive protocol for the preparation of nonhuman primate (NHP) neurosurgery using a novel combination of three-dimensional (3D) printing methods and MRI data extraction.

비인간 영장류의 신경 외과 계획을위한 MRI 기반 도구 상자

In this paper, we outline a method for surgical preparation that allows for the practical planning of a variety of neurosurgeries in NHPs solely using ...

Patient-Specific Polyvinyl Alcohol Phantom Fabrication with Ultrasound and X-Ray Contrast for Brain Tumor Surgery Planning

Phantoms are essential tools for clinical training, surgical planning and the development of novel medical devices. However, it is challenging to create anatomically accurate head phantoms with realistic brain imaging properties because standard fabrication methods are not optimized to replicate any patient-specific anatomical detail and 3D printing materials are not optimized for imaging properties. In order to test and validate a novel navigation system for use during brain tumor surgery, an anatomically accurate phantom with realistic imaging and mechanical properties was required. Therefore, a phantom was developed using real patient data as input and 3D printing of molds to fabricate a patient-specific head phantom comprising the skull, brain and tumor with both ultrasound and X-ray contrast. The phantom also had mechanical properties that allowed the phantom tissue to be manipulated in a similar manner to how human brain tissue is handled during surgery. The phantom was successfully tested during a surgical simulation in a virtual operating room.
The phantom fabrication method uses commercially available materials and is easy to reproduce. The 3D printing files can be readily shared, and the technique can be adapted to encompass many different types of tumor.

This protocol describes the fabrication of a patient specific skull, brain and tumor phantom. It uses 3D printing to create molds, and polyvinyl alcohol (PVA-c) is used as the tissue mimicking material.

뇌종양 수술 계획을 위한 초음파 및 엑스레이 대비를 가진 환자 특정 폴리비닐 알콜 팬텀 제조

Phantoms are essential tools for clinical training, surgical planning and the development of novel medical devices. However, it is challenging to create ...

Voxel Printing Anatomy: Design and Fabrication of Realistic, Presurgical Planning Models through Bitmap Printing

Most applications of 3-dimensional (3D) printing for presurgical planning have been limited to bony structures and simple morphological descriptions of complex organs due to the fundamental limitations in accuracy, quality, and efficiency of the current modeling paradigm. This has largely ignored the soft tissue critical to most surgical specialties where the interior of an object matters and anatomical boundaries transition gradually. Therefore, the needs of the biomedical industry to replicate human tissue, which displays multiple scales of organization and varying material distributions, necessitate new forms of representation. 
Presented here is a novel technique to create 3D models directly from medical images, which are superior in spatial and contrast resolution to current 3D modeling methods and contain previously unachievable spatial fidelity and soft tissue differentiation. Also presented are empirical measurements of novel, additively manufactured composites that span the gamut of material stiffnesses seen in soft biological tissues from MRI and CT. These unique volumetric design and printing methods allow for deterministic and continuous adjustment of material stiffness and color. This capability enables an entirely new application of additive manufacturing to presurgical planning: mechanical realism. As a natural complement to existing models that provide appearance matching, these new models also allow medical professionals to "feel" the spatially varying material properties of a tissue simulant-a critical addition to a field in which tactile sensation plays a key role.

This method demonstrates a voxel-based 3D printing workflow, which prints directly from medical images with exact spatial fidelity and spatial/contrast resolution. This enables the precise, graduated control of material distributions through morphologically complex, graduated materials correlated to radiodensity without loss or alteration of data.

복셀 인쇄 해부학 : 비트 맵 인쇄를 통해 사실적이고 사전 수술 계획 모델의 설계 및 제작

Most applications of 3-dimensional (3D) printing for presurgical planning have been limited to bony structures and simple morphological descriptions of ...

3D Scanning Technology Bridging Microcircuits and Macroscale Brain Images in 3D Novel Embedding Overlapping Protocol

The human brain, being a multiscale system, has both macroscopic electrical signals, globally flowing along thick white-matter fiber bundles, and microscopic neuronal spikes, propagating along axons and dendrites. Both scales complement different aspects of human cognitive and behavioral functions. At the macroscopic level, MRI has been the current standard imaging technology, in which the smallest spatial resolution, voxel size, is 0.1&#8211;1 mm3. Also, at the microscopic level, previous physiological studies were aware of nonuniform neuronal architectures within such voxels. This study develops a powerful way to accurately embed microscopic data into a macroscopic map by interfacing biological scientific research with technological advancements in 3D scanning technology. Since 3D scanning technology has mostly been used for engineering and industrial design until now, it is repurposed for the first time to embed microconnectomes into the whole brain while preserving natural spiking in living brain cells. In order to achieve this purpose, first, we constructed a scanning protocol to obtain accurate 3D images from living bio-organisms inherently challenging to image due to moist and reflective surfaces. Second, we trained to keep speed to prevent the degradation of living brain tissue, which is a key factor in retaining better conditions and recording more natural neuronal spikes from active neurons in the brain tissue. Two cortical surface images, independently extracted from two different imaging modules, namely MRI and 3D scanner surface images, surprisingly show a distance error of only 50 &#956;m as mode value of the histogram. This accuracy is comparable in scale to the microscopic resolution of intercellular distances; also, it is stable among different individual mice. This new protocol, the 3D novel embedding overlapping (3D-NEO) protocol, bridges macroscopic and microscopic levels derived by this integrative protocol and accelerates new scientific findings to study comprehensive connectivity architectures (i.e., microconnectome).

This article introduces an experimental protocol using 3D scanning technology bridging two spatial scales: the macroscopic spatial scale of whole-brain anatomy imaged by MRI at &#62;100 &#956;m and the microscopic spatial scale of neuronal distributions using immunohistochemistry staining and a multielectrode array system and other methods (~10 &#956;m).

3D 소설 포함 프로토콜에서 마이크로 회로 및 매크로 스케일 뇌 이미지를 연결하는 3D 스캐닝 기술

The human brain, being a multiscale system, has both macroscopic electrical signals, globally flowing along thick white-matter fiber bundles, and ...

Comprehensive Autopsy Program for Individuals with Multiple Sclerosis

We describe a rapid tissue donation program for individuals with multiple sclerosis (MS) that requires scientists and technicians to be on-call 24/7, 365 days a year. Participants consent to donate their brain and spinal cord. Most patients were followed by neurologists at the Cleveland Clinic Mellen Center for MS Treatment and Research. Their clinical courses and neurological disabilities are well-characterized. Soon after death, the body is transported to the MS Imaging Center, where the brain is scanned in situ by 3 T magnetic resonance imaging (MRI). The body is then transferred to the autopsy room, where the brain and spinal cord are removed. The brain is divided into two hemispheres. One hemisphere is immediately placed in a slicing box and alternate 1 cm-thick slices are either fixed in 4% paraformaldehyde for two days or rapidly frozen in dry ice and 2-methylbutane. The short-fixed brain slices are stored in a cryopreservation solution and used for histological analyses and immunocytochemical detection of sensitive antigens. Frozen slices are stored at -80 &#176;C and used for molecular, immunocytochemical, and in situ hybridization/RNA scope studies. The other hemisphere is placed in 4% paraformaldehyde for several months, placed in the slicing box, re-scanned in the 3 T magnetic resonance (MR) scanner and sliced into centimeter-thick slices. Postmortem in situ MR images (MRIs) are co-registered with 1 cm-thick brain slices to facilitate MRI-pathology correlations. All brain slices are photographed and brain white-matter lesions are identified. The spinal cord is cut into 2 cm segments. Alternate segments are fixed in 4% paraformaldehyde or rapidly frozen. The rapid procurement of postmortem MS tissues allows pathological and molecular analyses of MS brains and spinal cords and pathological correlations of brain MRI abnormalities. The quality of these rapidly-processed postmortem tissues (usually within 6 h of death) is of great value to MS research and has resulted in many high-impact discoveries.

Multiple sclerosis is an inflammatory demyelinating disease with no cure. Analysis of brain tissue provides important clues to understanding the pathogenesis of the disease. Here we discuss the methodology and downstream analysis of MS brain tissue collected through a unique rapid autopsy program in operation at the Cleveland Clinic.

다발성 경화증을 가진 개별을 위한 포괄적인 부검 프로그램

We describe a rapid tissue donation program for individuals with multiple sclerosis (MS) that requires scientists and technicians to be on-call 24/7, 365 ...

Multicolor 3D Printing of Complex Intracranial Tumors in Neurosurgery

Three-dimensional (3D) printing technologies offer the possibility of visualizing patient-specific pathologies in a physical model of correct dimensions. The model can be used for planning and simulating critical steps of a surgical approach. Therefore, it is important that anatomical structures such as blood vessels inside a tumor can be printed to be colored not only on their surface, but throughout their whole volume. During simulation this allows for the removal of certain parts (e.g., with a high-speed drill) and revealing internally located structures of a different color. Thus, diagnostic information from various imaging modalities (e.g., CT, MRI) can be combined in a single compact and tangible object.
However, preparation and printing of such a fully colored anatomical model remains a difficult task. Therefore, a step-by-step guide is provided, demonstrating the fusion of different cross-sectional imaging data sets, segmentation of anatomical structures, and creation of a virtual model. In a second step the virtual model is printed with volumetrically colored anatomical structures using a plaster-based color 3D binder jetting technique. This method allows highly accurate reproduction of patient-specific anatomy as shown in a series of 3D-printed petrous apex chondrosarcomas. Furthermore, the models created can be cut and drilled, revealing internal structures that allow for simulation of surgical procedures.

The protocol describes the fabrication of fully colored three-dimensional prints of patient-specific, anatomical skull models to be used for surgical simulation. The crucial steps of combining different imaging modalities, image segmentation, three-dimensional model extraction, and production of the prints are explained.

신경 외과에서 복잡한 두개내 종양의 다색 3D 프린팅

Three-dimensional (3D) printing technologies offer the possibility of visualizing patient-specific pathologies in a physical model of correct dimensions. ...

의학

뇌 질환의 신경영상 분석 강화

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.

저자 스포트라이트: Bridging Gaps in Anatomy and Establishing a Foundation for Algorithmic Studies (해부학의 격차 해소 및 알고리즘 연구의 기초 구축) 

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.

뇌 MRI를 사용한 인간 맥락총의 수동 분할

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

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뇌 MRI를 사용한 인간 맥락총의 수동 분할

뇌 MRI를 사용한 인간 맥락총의 수동 분할