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.

Burada özetlenen protokol MRG ve histoloji bölümleri arasında doğru bir karşılaştırma sağlar. protokol, marmosetler ve kemirgenler olarak insanlara veya küçük hayvanların beyinlerinde uygulanabilir birleşik biçiminde sunulmaktadır. büyük (insan) özgü ve beyinleri vurgulanır (insan dışı primat ve kemirgen), küçük ve beraberindeki video ve şekillerde farklılıklar biz marmoset uygulamayı göstermektedir. yaklaşım, basit olmasına rağmen, bu yöntem birçok adım hem de yazılımın çeşitli türleri kullanılmasını gerektirir. Ayrıca, potansiyel olarak bu yöntemin doğruluğunu etkileyen çeşitli sorunlar söz önemlidir. In vivo MR görüntü kalitesi önemli bir faktördür. MRG ve dijitalleşen histoloji görüntüleri arasında görüntü çözünürlüğünde eşitsizliği en aza indirmek için, mümkün olan en küçük MR voksel boyutu kullanılmalıdır. Bu kavram aynı zamanda postmortem MR görüntü kalitesi için de geçerlidir. artarkenpostmortem MRG kazanım süresi hazırlık böyle hava kabarcıkları ile ilgili odak sinyal terkinde gibi görüntü eserler tanıtabilirsiniz, çok daha yüksek görüntü çözünürlüğü sağlar. Bu eserler dokusunu belirsiz yanı sıra konturu etkileyebilir. Dahası, postmortem MR doku boyutları tespit süreci ve süresine göre etkilenme olasılığı vardır. In vivo, ex vivo MR maçı yakından edinimi sırasında dilim geometri kurulumunda anatomik yerlerinden kullanarak yaklasık edilebilir olsa da, doğrusal olmayan bir kayıt hala bu iki MR görüntüleri eşleşen bir doğruluk yüksek derecede ulaşmak için gerekli olacaktır. Beyin tutucu ve dilimleme makinesi tasarımı da çok önemli bir adımdır. Beynin dijital model yaratırken, bir yumuşatma algoritması biraz sabit beyne modeli göreceli büyütür olduğu uygulanır. Bu, tutucu ve dilimleme makinesi içine beynin kolay takılmasını sağlar ve tutucu keskin kenarları azaltır ve# 39; ın kontur. Model çok büyükse Ancak, (örneğin, daha fazla% 5), beyin postmortem MR ve / veya kesit sırasında hareket edebilir. Bir diğer önemli nokta Beyincik düzgün 3D baskılı nesnenin içine yerleştirilir ve böylece beyin modelinin tasarımını adapte etmektir. Beyincik otopside beyin çekimi sırasında zarar görmüşse, bu özellikle zor olabilir. Beyin dilimleme makinesi ve tutucu yazdırırken, 3D yazıcı türü de dikkatle seçilmelidir. Bazı çoklu püskürtmeli yazıcılar destek malzemesi çıkarmak için bir fırın kullanarak post-processing gerektirir. bu yazıcıların su geçirmez ve masaüstü erimiş birikim modelleme (FDM) yazıcılara göre nispeten daha dayanıklı nesneleri üretmek mümkün olmakla birlikte, ısıtma işlemi beyin kontur mükemmel dik olmayan bıçak boşlukları oluşturarak, biraz kutuyu çözgü destekleri kaldırın. Beyin kesit işlemi başka önemli bir adımdır. th kesme öncee levhalar halinde tüm beyin, beyin, beyin dilimleme makinesi içinde sıkıca oturuyor emin olmak için önemlidir: hafif basınç beynin üzerine tatbik edilir hiçbir hareket olmamalıdır. Bu mümkün bıçakları araştırmacılar tarafından belirlenen kesin bir yerde beyin aracılığıyla kesmek için yapacaktır. keserken sürekli, dengeli basınç hem bıçak sahiplerine uygulanmalıdır. Bıçakların netlik ve doku sertliğine bağlı olarak, hafif çapraz kesim hareketi düz kesim yüzeylerini korumak için avantajlı olabilir. parafin gömme işlemi de MRG ve histoloji arasındaki hiza bir kaynak olabilir. Doku levha gömme işlemi sırasında kaset karşı düz oturan değilse, microtome kesme düzleminin ve levhanın yüzey yeri arasında bir eğim olacak. Bu, tüm doku maruz kaldığı düz uçağı bulmak için kullanılamaz bölümleri kesme gerektirecektir. eğilmelerini düzeltmek için bir yolduryüksek izotropik çözünürlüklü postmortem MR görüntüleme düzlemin açısını değiştirerek gereğidir. Ancak, bu genellikle anizotropik çözünürlük (genellikle kalın koronal dilim) ile kazanılır in vivo MR gerçekleştirmek neredeyse imkansızdır. Son olarak, doku, yanı sıra (kırışıklık, çatlama, katlama) slaytlar hazırlanması sırasında formalin sabitleme dönemi ve parafine (büzülme) sırasında bazı deformasyon yaşayabilirsiniz. Bu deformasyonlar bazıları Slaytlarınıza aktarmadan önce bir su banyosunda 4-5 mikron bölümleri koyarak düzeltilebilir. Diğer deformasyonlar kısmen postmortem MR görüntüleri histolojik dijital görüntülerin deforme olabilen görüntü coregistration yaparak çözülebilir. Bununla birlikte, dikkatli ve yetenekli uygulama ile deformasyonları en aza bölümleri histoloji için MRG hacimleri eşleşen en etkili yaklaşımdır. Sonuç olarak, burada sunulan metodoloji inv sağlarestigators doğru MRG bulguları altta yatan patolojiyi değerlendirmek için. Daha genel olarak, tanımlanması ve / veya iltihap veya remiyelinizasyon gibi belirli patolojik süreçler, hedef araştırmalar için yeni MR biyobelirteçlerini doğrulamak için umut verici bir yaklaşımdır.

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.

Bu yöntemin akışı beyin dilimlenmiş sonra, plakların yüzeysel yüzeylerin MR görüntüleri ve resimler arasında görsel bir karşılaştırma birden plaka üzerinde iyi bir yönlendirme maçı (Şekil 2) gösteren Şekil 1&#39;de özetlenmiştir. levhalar parafine gömülü sonra, bir mikrotom üzerinde kesitlere ayrıldı ve boyanır. yüksek çözünürlüklü postmortem MR ve lekeli histoloji bölümleri arasında daha kapsamlı karşılaştırma marmoset beynin bütün yapılar arasında bir doğru ve tutarlı maç (Şekil 3) göstermektedir. MS bu hayvan modelinde, hayvanlar serebral beyaz cevher yayılmış beyaz cevher lezyonları gelişir. Bu lezyonlar MR yaparak noninvaziv tespit edilebilir. Şekil 4 MRG bulguları patolojik alt tabakayı aydınlatmak için bu tekniğin yeteneğini gösterir. In vivo MR tespit Küçük lezyonlar olabilirpostmortem MR ve histoloji hem izlenebilir. ilavelerde gösterildiği gibi, lezyonlar içinde demiyelinizasyon (çevre dokuya kıyasla hiperintensitesi) MR sinyal değişikliği sürüş ana bileşenlerinden biridir. Histoloji ve postmortem MR da in vivo MR (Şekil 4) üzerinde cevapsız lezyonları gösterebilir. <img alt="Şekil 1" src="/files/ftp_upload/54780/54780fig1.jpg" /> Bir marmoset beyin dilimleyici kutusu oluşturmak için 1. iş akışı Şekil. Beyin formalin (A1) ve T2 ağırlıklı MR kenar başına 150 mikron (A2) izotropik vokseller ile kazanılır ile sabittir. Görüntüler işlenir ve bir ikili maske (A3) oluşturmak için eşiklenir edilir. Yüzey daha sonra 3D modelleme yazılımı (A4) işlenir. Bir dilimleyici şablonuna ve beyin modeli arasında bir Boole çıkarma beyin dilimleme makinesi (B1) bir dijital modelini oluşturur. Beyin dilimleyici kutusu 3D yazıcı (B2) yazılıdır. Beyin sonra dilimleyici kutusuna sıkıca yerleştirilirKesme (B3). <a href="http://ecsource.jove.com/files/ftp_upload/54780/54780fig1large.jpg" target="_blank">Bu rakamın büyük halini görmek için lütfen buraya tıklayınız.</a> <img alt="şekil 2" src="/files/ftp_upload/54780/54780fig2.jpg" /> Şekil 2. Soldan sağa: in vivo MRI, postmortem MR ve doku döşeme fotoğrafı. Dilimleme uçaklar tekabül eden in vivo MR dilim (A) ile karşılaştırıldığında görsel postmortem MR (B) dayalı olarak kurulmuş ve bulundu. Daha sonra beyin kesilir ve elde edilen levhalar uyumlu (C) olduğu tespit edildi. <a href="http://ecsource.jove.com/files/ftp_upload/54780/54780fig2large.jpg" target="_blank">Bu rakamın büyük halini görmek için lütfen buraya tıklayınız.</a> <img alt="Şekil 3," src="/files/ftp_upload/54780/54780fig3.jpg" /> Şekil 3. Yüksek çözünürlüklü postmortem MR ve histolojibölüm eşleştirme. Levhalar 4 um bölüme bir mikrotom ile kesilmiş, ve hızlı mavi ve mor kresil (B) ile boyanmış parafin içine gömülmüştür. Kesitler daha sonra görsel 100 mikron T2 * beyin yapıları (A) dayalı MRG -ağırlıklı ile eşleştirildi. Bu Görüntüyü elde etmek için Ayrıntılar protokol ve Tablo 1. Beyin yapılarının ek bölümünde şunlardır: (1) kırmızı ok = iç kapsül, mavi ok = ön komissür; (2) kırmızı ok = putamen, mavi ok = optik sistem; (3) kırmızı ok = kaudat, mavi ok = hipokampus; (4) kırmızı ok = korpus kallosum, mavi ok = serebral su kemeri; (5) kırmızı ok = aşağı kollikulus, mavi ok = piramidal sistem. B1 kesikli kutu, ya beyin kesme veya parafine sırasında bir hata solda ön komissürün uyumsuzluğu yol Y ekseni etrafında hafif bir rotasyon nedeniyle bir dilim gösterir. <a href="http://ecsource.jove.com/files/ftp_upload/54780/54780fig3large.jpg" target="_blank">Bir görmek için buraya tıklayınız</a>Bu rakamın daha büyük bir versiyonu. <img alt="Şekil 4," src="/files/ftp_upload/54780/54780fig4.jpg" /> Şekil 4. histoloji bölümüne in vivo MR gelen lezyonlar izleniyor. In vivo MR ya optik yolu (A1) lezyonları önermek için anormal hiperintensitesi sinyalinin hiçbir inandırıcı kanıt gösterdi. Ancak, yüksek çözünürlüklü postmortem MR hem optik yolları (A2) açık hiper yoğun çizgiler görünüyor. 4 mikron histoloji bölümünün hızlı mavi / mor cresyl leke ex vivo MR görülen hiperintens alanlar (A3) demiyelinize olduğunu göstermektedir. Serebral beyaz cevherde, in vivo MR ince bilateral hiperintensitesi (B1, ilavelerde büyütülmüş) gösterir. hiperintens alanlar yüksek çözünürlüklü postmortem MR (B2) daha açıktır. 4 um&#39;lik histoloji bölümünün LFB leke Bu alanlar (B3) demiyelinize olduğunu göstermektedir. Bazal i ile karşılaştırıldığında sonran vivo MR ve hemotoksilin-ve-eozin boyama, sağ taraf anatomik bir anormallik, bir miyelin kaybetmiş lezyon olduğu belirlenmiştir. <a href="http://ecsource.jove.com/files/ftp_upload/54780/54780fig4large.jpg" target="_blank">Bu rakamın büyük halini görmek için lütfen buraya tıklayınız.</a> <img alt="Yan kod dosyaları" src="/files/ftp_upload/54780/54780supplementalfiles.jpg" /> Yan kod dosyaları. Brain_Slicer_Parts_Marmoset.stl: <a href="https://www.jove.com/files/ftp_upload/54780/Brain_Slicer_Parts_Marmoset.stl" target="_blank">Bu dosyayı indirmek için tıklayınız.</a> Brain_Slicer_Parts_Human.stl: <a href="https://www.jove.com/files/ftp_upload/54780/Brain_Slicer_Parts_Human.stl" target="_blank">Bu dosyayı indirmek için tıklayınız.</a> Cap_Insert.stl: <a href="https://www.jove.com/files/ftp_upload/54780/Cap_Insert.stl" target="_blank">Bu dosyayı indirmek için tıklayınız.</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

Bu protokolün genel amacı doğru özelleştirilmiş 3D baskılı beyin sahipleri ve dilimleme kutuları oluşturulması yoluyla histoloji bölümleri ile manyetik rezonans görüntüleme (MRG) görüntü hacimleri hizalamak.

3D Baskı Teknolojisini kullanan Histoloji ile MRG Birleştirme: Beyin için Protokol Kesit

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

Research

JoVE Journal

Neuroscience

14.8K Görüntüleme.  National Institute of Neurological Disorders and Stroke.  Bu protokolün genel amacı doğru özelleştirilmiş 3D baskılı beyin sahipleri ve dilimleme kutuları oluşturulması yoluyla histoloji bölümleri ile manyetik rezonans görüntüleme (MRG) görüntü hacimleri hizalamak. 

Video: 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.

Teşhis ve Tedavi İzleme Nanomalzemelerin Kayıtlı bio

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

Biyomühendislik

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.

İnsanlar ve Mouse Periventriküler Doku Yanal ventrikülleri ve histolojik Karakterizasyonu 3D Modelleme

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

Nörobilim

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.

İnsan olmayan Primatlarda Nöroşirürji Planlaması için MRI Tabanlı Araç Kutusu

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.

Beyin Tümörü Cerrahisi Planlaması için Ultrason ve X-Ray Kontrastı ile Hastaya Özel Polivinil Alkol Phantom İmalatı

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.

Voxel Baskı Anatomisi: Bitmap Baskı Ile Gerçekçi, Presurgical Planlama Modellerinin Tasarımı ve İmalatı

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 tarama teknolojisi köprüleme mikrodevreler ve Macroscale beyin görüntüleri 3D roman gömme çakışan protokol

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.

Multipl skleroz bireyler için kapsamlı otopsi programı

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.

Nöroşirürjide Kompleks İntrakraniyal Tümörlerin Çok Renkli 3D Baskısı

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

Tıp

Beyin Bozukluklarında Nörogörüntüleme Analizinin Geliştirilmesi

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.

Yazar Spotlight: Anatomideki Boşlukları Kapatmak ve Algoritmik Çalışmalar İçin Bir Temel Oluşturmak 

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.

Beyin MRG Kullanılarak İnsan Koroid Pleksusunun Manuel Segmentasyonu

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

3D Baskı Teknolojisini kullanan Histoloji ile MRG Birleştirme: Beyin için Protokol Kesit

Özet

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Teşhis ve Tedavi İzleme Nanomalzemelerin Kayıtlı bio

İnsanlar ve Mouse Periventriküler Doku Yanal ventrikülleri ve histolojik Karakterizasyonu 3D Modelleme

İnsan olmayan Primatlarda Nöroşirürji Planlaması için MRI Tabanlı Araç Kutusu

Beyin Tümörü Cerrahisi Planlaması için Ultrason ve X-Ray Kontrastı ile Hastaya Özel Polivinil Alkol Phantom İmalatı

Voxel Baskı Anatomisi: Bitmap Baskı Ile Gerçekçi, Presurgical Planlama Modellerinin Tasarımı ve İmalatı

3D tarama teknolojisi köprüleme mikrodevreler ve Macroscale beyin görüntüleri 3D roman gömme çakışan protokol

Multipl skleroz bireyler için kapsamlı otopsi programı

Nöroşirürjide Kompleks İntrakraniyal Tümörlerin Çok Renkli 3D Baskısı

Beyin MRG Kullanılarak İnsan Koroid Pleksusunun Manuel Segmentasyonu

Beyin MRG Kullanılarak İnsan Koroid Pleksusunun Manuel Segmentasyonu