Name: Segmentation of the Choroid Plexus Using Manual Delineations
Uploaded: 2023-12-15T12:40:00
Description: Watch this Scientific Journal Video about Segmentation of the Choroid Plexus Using Manual Delineations at JoVE.com

segmentation of the choroid plexus using manual delineations

Migliorare l'analisi di neuroimaging nei disturbi cerebrali

Choroid plexus function 
The choroid plexus is a highly vascularized structure in the brain consisting of fenestrated capillaries and a monolayer of choroid plexus epithelial cells1. The choroid plexus projects into the lateral, third, and fourth cerebral ventricles and produces cerebrospinal fluid (CSF), which plays an important role in neural patterning2 and brain physiology3,4. The choroid plexus secretes neurovascular substances, encompasses a stem-cell like repository, and acts as a physical barrier to impede the entrance of toxic metabolites, an enzymatic barrier to remove moieties that circumvent the physical barrier, and an immunological barrier to protect against foreign invaders5. The choroid plexus modulates neurogenesis6, synaptic plasticity7, inflammation8, circadian rhythm9,10, gut brain-axis11, and cognition12. Moreover, peripheral cytokines, stress, and infection (including SARS-CoV-2) can disrupt the blood-CSF barrier13,14,15,16. Thus, the choroid plexus-CSF system is integral for neurodevelopment, neurocircuit maturation, brain homeostasis, and repair17. Since immune, inflammatory, metabolic, and enzymatic alterations impact the brain, researchers are using neuroimaging tools to assess the role of the choroid plexus across the lifespan and in brain disorders18,19,20. However, limitations exist in commonly used automated tools for choroid plexus segmentation, such as FreeSurfer, which result in the choroid plexus being poorly segmented. Thus, there is a critical need for ground truth manual segmentation of the choroid plexus that can be used to develop an accurate automated tool for choroid plexus segmentation.
Choroid plexus in neurodevelopment and brain disorders 
The role of the choroid plexus in brain disorders has long been neglected, mainly because it was regarded as a supporting player whose role was to cushion the brain and maintain a proper salt balance2,21. However, the choroid plexus has gained attention as a structure linked to brain disorders such as pain syndromes22, SARS-CoV-216,23,24, neurodevelopmental2, and brain disorders19, suggesting a transdiagnostic effect in the development of behavioral disorders. In neurodevelopmental disorders, choroid plexus cysts were associated with an increased risk of developmental delay, attention-deficit/hyperactivity disorder (ADHD), or autism spectrum disorder (ASD)25,26. Additionally, lateral ventricle choroid plexus volume was found to be increased in patients with ASD27. In brain disorders,choroid plexus abnormalities have been described since 1921 in psychotic disorders28,29. Previous studies have identified choroid plexus enlargement using FreeSurfer segmentation in a large sample of patients with psychotic disorders compared to both their first-degree relatives and controls19. These findings were replicated using manually segmented choroid plexus volume in a large sample of clinical high-risk for psychosis population and found that these patients had larger choroid plexus volume compared to healthy controls30. There are a growing number of studies demonstrating choroid plexus enlargement in complex regional pain syndrome22, stroke31, multiple sclerosis20,32, Alzheimer&#39;s33,34, and depression35, with some demonstrating a link between peripheral and brain immune/inflammatory activity. These neuroimaging studies are promising; however, poor lateral ventricle choroid plexus segmentation by FreeSurfer21 limits the trustworthiness of automated choroid plexus volume estimation. As a result, studies in multiple sclerosis20,32, depression35, Alzheimer&#39;s34, and early psychosis36 have begun manually segmenting the lateral ventricle choroid plexus, but there are no current guidelines for how to do this, nor is their guidance on segmenting the third and fourth ventricle choroid plexus.
Common segmentation tools exclude the choroid plexus 
Brain segmentation pipelines such as FreeSurfer37,38,39, FMRIB Software Library (FSL)40, SLANT41, and FastSurfer (developed by the co-author Martin Reuter)42,43, accurately and reliably segment cortical and subcortical structures employing atlas-based (FSL), atlas- and surface-based (FreeSurfer), and deep learning segmentation paradigms (SLANT and FastSurfer). Weaknesses of some of these approaches include processing speed, limited generalization to different scanners, field strengths and voxel sizes37,44, and forced alignment of the label map in a standard atlas space. However, the capability to segment the choroid plexus and the compatibility with high-resolution MRI is only addressed by FreeSurfer and FastSurfer. The neural networks behind FastSurfer, are trained on FreeSurfer choroid plexus labels, so they inherit FreeSurfer&#39;s previously discussed reliability and coverage limitations, with the third and fourth ventricles being ignored21. Current limitations for high-resolution MRI also exist, but FreeSurfer&#39;s high-resolution stream45 and FastSurferVINN43 can be used to handle this issue.
Current choroid plexus segmentation tools 
There is only one freely available segmentation tool for the choroid plexus, but segmentation accuracy is limited. Accurate choroid plexus segmentation can be impacted by a variety of factors, including (1) variability in choroid plexus location (spatially non-stationary) due to its location within the ventricles, (2) differences in voxel intensity, contrast, resolution (within-structure heterogeneity) due to cellular heterogeneity, dynamic choroid plexus function, pathological changes, or partial volume effects, (3) age- or pathology-related ventricular size differences impacting choroid plexus size, and (4) proximity to adjacent subcortical structures (hippocampus, amygdala, caudate, and cerebellum), which are also difficult to segment. Given these challenges, FreeSurfer segmentations often under or over-estimate, mislabel or ignore the choroid plexus.
Three recent publications addressed the gap of reliable choroid plexus segmentation with a Gaussian Mixture Model (GMM)46, an Axial-MLP47, and U-Net-based deep learning approaches48. Each model was trained and evaluated using private, manually labeled datasets of at most 150 subjects with a limited diversity of scanners, sites, demographics, and disorders. While these publications46,48,49 achieved significant improvements over FreeSurfer&#39;s choroid plexus segmentation - sometimes doubling the intersection of prediction and ground truth, neither method is (1) validated in high-resolution MRI, (2) has dedicated generalization and reliability analyses, (3) features large representative training and testing datasets, (4) specifically addresses or analyzes choroid plexus segmentation challenges such as partial volume effects, or (5) is publicly available as a ready-to-use tool. Thus, the current &#34;gold standard&#34; for choroid plexus segmentation is manual tracing, e.g., using 3D Slicer50 or ITK-SNAP51, which has not been previously described and has been a major challenge for researchers wishing to examine the role of the choroid plexus in their studies. 3D Slicer was chosen for manual segmentation due to the author&#39;s familiarity with the software and because it provides the user with various tools based on different approaches that can be combined to obtain the desired result. Other tools can be used, such as ITK-SNAP, which is primarily oriented on image segmentation, and once the tool is mastered, good results can be obtained by the user. Additionally, the authors have conducted a case-control study demonstrating the high accuracy and reliability of their manual segmentation technique using 3D Slicer30, and that specific methodology is described herein.

Autore in primo piano: colmare le lacune nell'anatomia e stabilire una base per gli studi algoritmici 

Segmentazione manuale del plesso coroideo umano mediante risonanza magnetica cerebrale

We aim to establish an accessible and standardized protocol for manually segmenting the choroid plexus within the lateral third and fourth ventricles of the brain. We hope to address any common questions or problems that can arise when manually segmenting the choroid plexus, especially considering the complex nature of its location within the brain. Developing this protocol will lead to the creation of a large enough data set consisting of ground truth segmentation maps that we can then use to train and develop algorithms that can accurately and automatically segment the choroid plexus.In the future, this will lead to studies that investigate the role of the choroid plexus within various neurologic and neuropsychiatric disorders.

Watch this Scientific Journal Video about Segmentation of the Choroid Plexus Using Manual Delineations at JoVE.com

Segmentation of the Choroid Plexus Using Manual Delineations  

Segmentazione del plesso coroideo mediante delineazioni manuali

Per iniziare, importa l'imaging digitale e le comunicazioni in medicina o i dati DICOM facendo clic sul pulsante DCM situato nell'angolo in alto a sinistra della barra degli strumenti e facendo clic sul pulsante Importa file DICOM. Per regolare la luminosità di un'immagine, fare clic su Regola finestra e livello di volume oppure fare clic con il pulsante sinistro del mouse sull'immagine e trascinare il mouse verso l'alto o verso il basso. Quindi fare clic con il pulsante sinistro del mouse sulla porzione dell'immagine e spostare il mouse a sinistra o a destra per regolare il contrasto.Fare riferimento ai nuclei profondi della materia grigia o alle barre della scala di contrasto dell'intensità del segnale e assicurarsi che rimanga coerente durante la segmentazione per scegliere il contrasto adatto per il plesso coroideo. Per avviare la segmentazione del plesso coroideo laterale del terzo e quarto ventricolo, selezionare l'editor dei segmenti dal menu a discesa del modulo. Ora fai clic sul menu a discesa per la segmentazione per selezionare diverse segmentazioni e rinominare quella selezionata.Utilizzare il menu a discesa del volume principale e selezionare i set NIfTI o DICOM da modificare. Fare clic due volte sul pulsante Aggiungi per includere due segmenti per il plesso coroideo del ventricolo laterale. Fare doppio clic sui loro titoli e rinominarli come plesso coroideo del ventricolo laterale destro e plesso coroideo del ventricolo laterale sinistro.Fare nuovamente clic sul pulsante Aggiungi per introdurre segmenti per il plesso coroideo del terzo e quarto ventricolo. Successivamente, rinominali rispettivamente come plesso coroideo del terzo ventricolo e plesso coroideo del quarto ventricolo. Iniziare con il plesso coroideo del ventricolo laterale sul piano assiale e assicurarsi di posizionare le immagini in base alla linea bicommissurale.Utilizzare il trigonum collaterale come punto di riferimento per localizzare il plesso coroideo del ventricolo laterale. Per avviare la segmentazione manuale, seleziona lo strumento Disegno o Disegno che si trova nella sezione Effetti dell'editor dei segmenti. Durante l'utilizzo dello strumento di disegno, selezionare il diametro del pennello desiderato per la pittura.Utilizzare il livello del nucleo rosso per determinare quando interrompere la segmentazione del plesso coroideo nei ventricoli laterali. Per localizzare il plesso coroideo del terzo ventricolo, iniziare dal piano sagittale e utilizzare il forame di Monro, il fornice, il corpo calloso, il talamo e la vena cerebrale interna come punti di riferimento. Allo stesso modo, per il plesso coroideo del quarto ventricolo, iniziare dal piano sagittale e utilizzare il peduncolo cerebellare superiore, il ponte e il midollo come punti di riferimento per individuare il plesso coroideo nel quarto ventricolo.Dal menu a discesa dei moduli, vai a quantificazione e seleziona statistiche di segmento. Quindi, nella sezione di input, seleziona la mappa di segmentazione appena creata per la quantificazione nello strumento di segmentazione e seleziona il volume MRI dal volume dello scaler. Per la tabella di output, seleziona l'opzione table in output e premi applica.Apparirà una tabella che mostra il volume del plesso coroideo in diverse unità. Fare clic sul pulsante Salva situato nella parte in alto a sinistra della barra degli strumenti per memorizzare i file generati. Conserva i file di segmentazione nei formati nrrd, nii.GZ, o TSV.

Research

JoVE Journal

Neuroscience

Segmentation of the Choroid Plexus Using Manual Delineations

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 ...