processing micro-ct scanned image of stained murine neonatal brain sample

Mus neonatal hjerne mikro-CT-skanning og bildebehandling

Micro-computed tomography (micro-CT) imaging is a valuable tool for different fields of research. In biology, it is especially suitable for bone research because of X-ray absorption in mineralized tissues. Due to this feature, diverse questions regarding bone development1, metabolism2, and evolution3,4, among other topics, have been approached with the assistance of micro-CT. In 2008, de Crespigny et al.5 showed that micro-CT images of adult mouse and rabbit brains could be obtained using iodine as a contrast agent. This work opened a new application for this imaging technique, since iodine allowed the acquisition of images from soft tissues which otherwise would be insensitive to X-rays. Thus, the general goal of combining micro-CT and an iodine-based contrast agent is to obtain high-resolution images, in which soft tissues can be distinguished and identified at a meso or macro anatomical level.
This technique has notable potential for studies that require detailed ex vivo phenotypic characterization of small specimens, such as mouse embryos, which are widely used in experimental designs6. Iodine contrast in combination with micro-CT imaging has been used to obtain volumetric quantifications of organs7 and landmark three-dimensional (3D) structures8,9. In recent years, micro-CT scanning of stained samples has been applied to describe brain phenotypic features of rodents10, and different improvements to the technique have been proposed. For adult brains, a protocol of 48 h of immersion in iodine, with a previous step of perfusion with a hydrogel, was found to produce images of high quality11. Gignac et al.12 expanded the limits of this technique by showing that rat brains stained with iodine could be processed to perform routine histological techniques. Similarly, these procedures demonstrate promising results for embryonic and pre-weaning rodent brains8,13,14,15.
Although neuroscience has largely applied microscope-based techniques to assess different structural and functional aspects of brain development, such studies are more suitable for characterizing specific cell populations or spatially limited structures. Conversely, micro-CT imaging allows the description of whole structures and the acquisition of 3D models that preserve relevant spatial information, which is complementary to microscopic techniques. Magnetic resonance imaging (MRI) is also a standard technique applied to explore the structural features of small animals16,17,18. However, micro-CT, with the use of a contrast agent, has two main advantages for ex vivo fixed samples: micro-CT scanners are largely less expensive and easy to operate, and allow a higher spatial resolution than MRI12.
This work aims to describe the procedure to obtain high-resolution images from neonatal mouse brains using micro-CT scanning after staining with Lugol&#39;s solution, an iodine-based contrast agent. A comprehensive protocol is presented, which starts with preliminary stages such as sample collection and fixation of tissues, and goes through staining, micro-CT image acquisition, and standard processing. Image processing includes the segmentation of a 3D volume of the complete head, as well as of the brain, and the selection of specific anatomical planes to digitize point coordinates that could be then used in morphometric analyses. Although the focus here is the neonatal mouse brain, similar strategies can be applied to other soft tissues. Thus, the protocol presented here is flexible enough to be applied, with subtle modifications, to other types of samples.

Forfatter Spotlight: Høyoppløselig avbildning av musenyfødte hjerner – en mikro-CT-protokoll med Lugols løsningskontrastmiddel

Micro-CT bildebehandling og morfometrisk analyse av mus neonatale hjerner

In experimental neuroscience, specifically for those studies addressing questions about development, it is relevant to count on quantitative characterization of brains of embryonic and prenatal specimens. Micro computed tomography in combination with a common contrast agent is capable of producing high solution images suitable for further morphometric analysis. Micro computed tomography has been applied to imaging hard tissue such as bone because of x-ray absorption in mineralized tissues.However, in the last decades, the use of Lugol's solution as a contrast agent has upgraded the application of using machine technique for soft tissues. This protocol combines procedures and tools using the field to demonstrate the great potential of micro computed tomography for studying the prenatal brains of small animals. The strength of our proposal, precisely depicting the process from the sample preparation to morphometric data processing.Images derived from micro computed tomography preserve a special information, which is difficult with standard histological techniques. Additionally, micro computed tomography with the use of a contrast agent has two advantages when compared with magnetic resonance. Scanners are less expensive and easy to operate and allow a higher spatial resolution.The protocol presented here could be applied with subtle modifications to fix samples of different organs derived from diverse species. Then a variety of scientific questions could be approached. Since the contrast agent is administered by emersion, the main limitations should be related to the sample size, but the potential applications are enormous.

Behandling av mikro-CT-skannet bilde av farget murin neonatal hjerneprøve

For å begynne, start bildebehandlingsprogramvaren, velg fil, åpne deretter data og velg de tidligere genererte micro CT-skannede bildene i dot BMP-format. Når vinduet til bildet leseparametere åpnes, bekreft parametrene og godta om det er riktig. I hovedpanelet klikker du på prosjektvisning for å finne et nytt objekt opprettet med navnet på prikken BMP-filen.Høyreklikk på det opprettede objektet og velg alternativet orto-skive, og klikk deretter opprett. Under egenskaper velger du orienteringsplanet og stykkenummeret du vil se. For å få 3D-volumer av hele hodet i hovedpanelet, gå til prosjektvisning, høyreklikk bildeobjektet, velg det interaktive terskelalternativet og klikk opprett.Under egenskaper endrer du verdiene for minimum terskel RGB og maksimumsterskel RGB til den delen av bildet som svarer til dyrets hode er valgt. Velg deretter bruk. Høyreklikk på terskelobjektet opprettet under prosjektvisningen.Velg isosurface i egenskaper, velg en terskel for å visualisere overflaten, og klikk deretter på bruk. For å digitalisere landemerkene, høyreklikk på prosjektvisning, velg opprett objekt, velg deretter punkter og linjer etterfulgt av landemerker, og klikk deretter på opprett. Høyreklikk deretter landemerkene for det nye objektet.Velg landemerkevisning og klikk på opprett. Endre punktstørrelsen under størrelse. Hvis du vil legge til landemerker i egenskaper, velger du legg til i redigeringsmodus.Digitaliser fem likt fordelte punkter rundt kurvene til neste landemerke ved midthjernebarkkrysset, og digitaliser deretter åtte semilandemerker rundt cortex. For å lagre de digitaliserte punktene, høyreklikk på objektlandemerker og velg lagre data. For å segmentere hjernen, høyreklikk på prosjektvisning, etterfulgt av opprett objekt, velg bilder og felt, og deretter etikettfelt.Klikk på opprett. Velg etikettfeltobjektet, og trykk på segmenteringsredigeringsalternativet i egenskaper. Legg til et nytt materiale under materialer og gi det nytt navn til hjernen.Under utvelgelse velger du gjeldende stykke for å segmentere vevet som tilsvarer hjernen i hvert stykke. I verktøy, bruk tryllestaven og børsten for å velge hjernevevet i hvert stykke. Trykk deretter på legg til under valg.Gå nå tilbake til prosjektvisning, høyreklikk på etikettfeltet og velg generer overflate, og klikk deretter på bruk. Når overflaten er oppnådd, bruk ekstraktoverflaten for å eksportere den. Med mikro CT-skanning, til tross for den lille størrelsen på neonatale musehjerner, kan de anatomiske strukturer som olfaktoriske pærer, cortex, midbrain, cerebellum og bakhjerne skilles.Den manuelle segmenteringen av hele hjernen resulterte i 3D-modellrekonstruksjonen av den nyfødte hjernen.

Research

JoVE Journal

Neuroscience

Processing Micro-CT Scanned Image of Stained Murine Neonatal Brain Sample

Micro-CT Imaging and Morphometric Analysis of Mouse Neonatal Brains

Neuroimages are a valuable tool for studying brain morphology in experiments using animal models. Magnetic resonance imaging (MRI) has become the standard ...

Murine Neonatal Brain Sample Fixation and Staining for Micro-CT Scanning

Murine neonatal hjerneprøvefiksering og farging for mikro-CT-skanning