Name: large-scale reconstructions and independent, unbiased clustering based on morphological metrics to classify neurons in selective populations
Uploaded: 2017-02-15T12:30:00.000+00:00
Duration: 12 min 27 s
Description: Watch this Scientific Journal Video about Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations at JoVE.com

Vorremmo ringraziare il Dott. Ed Callaway e Marty Usrey per averci permesso di utilizzare il tessuto preparato come parte di uno studio preliminare e Libby Fairless e Shiyuan Liu per un aiuto con ricostruzioni neuronali. Questo lavoro è stato finanziato dal NIH (NEI: EY018683) e la Fondazione Whitehall.

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	<li>Cajal, S. R. y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Histologie du systeme nerveaux de l'homme et des vertebres. , (1911).</li><li>Seung, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+functional+connectomics.">Toward functional connectomics.</a> Nature. 471, 170-172 (2011).</li><li>Callaway, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transneuronal+circuit+tracing+with+neurotropic+viruses.">Transneuronal circuit tracing with neurotropic viruses.</a> Current Opinion in Neurobiology. 18, 1-7 (2009).</li><li>Wickersham, I. R., Finke, S., Conzelmann, K. K., Callaway, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retrograde+neuronal+tracing+with+a+deletion-mutant+rabies+virus.">Retrograde neuronal tracing with a deletion-mutant rabies virus.</a> Nature Methods. 4, 47-49 (2007).</li><li>Briggs, F., Kiley, C. W., Callaway, E. M., Usrey, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+substrates+for+parallel+streams+of+corticogeniculate+feedback+originating+in+both+V1+and+V2+of+the+macaque+monkey.">Morphological substrates for parallel streams of corticogeniculate feedback originating in both V1 and V2 of the macaque monkey.</a> Neuron. 90, 388-399 (2016).</li><li>Cauli, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Classification+of+fusiform+neocortical+interneurons+based+on+unsupervised+clustering.">Classification of fusiform neocortical interneurons based on unsupervised clustering.</a> PNAS. 97, 6144-6149 (2000).</li><li>Bragg, E. M., Fairless, E. A., Liu, S., Briggs, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphology+of+visual+sector+thalamic+reticular+neurons+in+the+macaque+monkey+sugests+retinotopically-specialized,+parallel+stream-mixed+input+to+the+lateral+geniculate+nucleus.">Morphology of visual sector thalamic reticular neurons in the macaque monkey sugests retinotopically-specialized, parallel stream-mixed input to the lateral geniculate nucleus.</a> J. Comparative Neurology. 525 (5), 1273-1290 (2017).</li><li>Osakada, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+rabies+virus+varients+for+monitoring+and+manipulating+activity+and+gene+expression+in+defined+neural+circuits.">New rabies virus varients for monitoring and manipulating activity and gene expression in defined neural circuits.</a> Neuron. 71, 617-631 (2011).</li><li>Callaway, E. M., Luo, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monosynaptic+circuit+tracing+with+glycoprotein-deleted+rabies+viruses.">Monosynaptic circuit tracing with glycoprotein-deleted rabies viruses.</a> Journal of Neuroscience. 35, 8979-8985 (2015).</li><li>Nhan, H. L., Callaway, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphology+of+superior+colliculus-+and+middle+temporal+area-projecting+neurons+in+primate+primary+visual+cortex.">Morphology of superior colliculus- and middle temporal area-projecting neurons in primate primary visual cortex.</a> J. Comparative Neurology. 520, 52-80 (2012).</li><li>Pinault, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+thalamic+reticular+nucleus:+structure,+function+and+concept.">The thalamic reticular nucleus: structure, function and concept.</a> Brain Research Reviews. 46, 1-31 (2004).</li><li>Gage, G. J., Kipke, D. R., Shain, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole+Animal+Perfusion+Fixation+for+Rodents.">Whole Animal Perfusion Fixation for Rodents.</a> Journal of Visualized Experiments. 65, e3564 (2012).</li><li>Wong-Riley, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+the+visual+system+of+monocularly+sutured+or+enucleated+cats+demonstrable+with+cytochrome+oxidase+histochemistry.">Changes in the visual system of monocularly sutured or enucleated cats demonstrable with cytochrome oxidase histochemistry.</a> Brain Research. 171, 11-28 (1979).</li><li>Gerfen, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Basic+neuroanatomical+methods.">Basic neuroanatomical methods.</a> Current Protocols in Neuroscience. Chapter 1, Unit 1.1 (2003).</li><li>Thorndike, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Who+belongs+in+the+family?.">Who belongs in the family?.</a> Psychometrika. 18, 267-276 (1953).</li><li>Talebi, V., Baker, C. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Categorically+distinct+types+of+receptive+fields+in+early+visual+cortex.">Categorically distinct types of receptive fields in early visual cortex.</a> Journal of Neurophysiology. 115, 2556-2576 (2016).</li><li>Helmstaedter, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Connectomic+reconstruction+of+the+inner+plexiform+layer+in+the+mouse+retina.">Connectomic reconstruction of the inner plexiform layer in the mouse retina.</a> Nature. 500, 168-174 (2013).</li></ol>

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studi neuroanatomici sono rimasti un pilastro di neuroscienze e recente interesse connectomics e le relazioni struttura-funzione ha rinnovato entusiasmo per la caratterizzazione morfologica dettagliata delle popolazioni di neuroni selettivi. Tradizionalmente, gli studi neuroanatomici hanno fatto affidamento su classificazioni qualitative di neuroni in classi morfologicamente distinte di neuroni definiti da neuroanatomisti esperti. Con i progressi nelle tecniche per la ricostruzione neuroni e l&#39;estrazione dei dati mo...

Neuroanatomy è uno dei fondamenti delle neuroscienze 1 e recente interesse &quot;connectomics&quot; ha rinnovato entusiasmo per la comprensione della diversità morfologica delle popolazioni neuronali e le connessioni tra i neuroni specifici 2. Metodi per l&#39;etichettatura e neuroni ricostruendo hanno notevolmente migliorato con le recenti innovazioni, tra cui genetica e virus-mediata circuito di tracciamento approcci 3, 4, consentendo studi morfologici più complete delle popolazioni neuronali 5. Oltre a miglioramenti nella etichettatura singoli neuroni, sono anche emerse tecniche di analisi quantitativa dei dati che consentono di classificazione indipendente e imparziale dei neuroni in sottopopolazioni distinte in base a dati morfologici 5, 6. Queste tecniche imparziali sono un miglioramento su più traditional metodi di classificazione qualitativi che sono stati lo standard nel settore per più di un secolo. L&#39;obiettivo di questo studio è quello di delineare, passo dopo passo, la combinazione di etichettatura virus-mediata di neuroni all&#39;interno di una popolazione selettivo, ricostruzioni su larga scala di un campione globale di questi neuroni, e l&#39;analisi quantitativa dei dati basata su cluster indipendente con valutazione statistica. Grazie alla combinazione di questi metodi, delineiamo un nuovo approccio verso la raccolta e l&#39;analisi dei dati neuroanatomici da facilitare la campionatura completa e imparziale la classificazione dei tipi di neuroni morfologicamente unici all&#39;interno di una popolazione neuronale selettiva. Come esempio di questi metodi, descriviamo la nostra analisi di una vasta popolazione di neuroni all&#39;interno di un singolo settore del nucleo reticolare del talamo (TRN) del macaco. Questi dati provengono da uno studio preliminare 7. Metodi per l&#39;etichettatura selettivamente i neuroni TRN proiettano al Latera dorsalil genicolato nucleo del talamo (dLGN) con iniezione chirurgica del virus della rabbia modificato codifica EGFP 4, 8 (vedi tabella di specifici materiali / attrezzature, fila 2) sono delineati. Questo virus della rabbia modificato manca il gene che codifica una proteina essenziale cappotto, eliminando movimento trans-sinaptica del virus. Una volta che il virus entra terminali degli assoni nel sito di iniezione, si comporta come un tracciante tradizionale retrograda con l&#39;importante vantaggio di guidare espressione EGFP durante l&#39;intero arborization dendritica dei neuroni infettati 5, 9, 10. Di conseguenza, questo virus della rabbia G-cancellato può essere utilizzato per infettare selettivamente etichettare qualsiasi popolazione neuronale dopo l&#39;iniezione e trasporto retrogrado. Per eseguire un&#39;analisi completa di una specifica popolazione neuronale, è importante campionareun&#39;ampia distribuzione dei neuroni all&#39;interno della popolazione. Poiché la tecnica di etichettatura virus-mediata produce completa intracellulare, &quot;Golgi-like&quot; riempie di molti neuroni con assoni nel sito di iniezione virus, è possibile ricostruire un campione molto ampio di neuroni nella misura massima di una struttura cerebrale. Inoltre, poiché il virus della rabbia modificato è così efficace a infettare ed etichettatura gran numero di neuroni, è possibile ricostruire centinaia di neuroni per animale. Procedure di campionamento 160 neuroni tutto il settore visivo del TRN 11 per generare un campione completo di dLGN sporgenti neuroni TRN sono delineati. Il processo di ricostruzione neuroni individuali utilizzando un sistema di ricostruzione neurone compreso un microscopio, fotocamera e software di ricostruzione è descritto. Anche descritto sono metodi per determinare le posizioni di singoli neuroni all&#39;interno di una struttura del cervello (in questo caso all&#39;interno del TRN) e per verificare il virus iniezione site dal volume e all&#39;interno di una struttura (in questo caso all&#39;interno del dLGN) utilizzando ricostruzioni contorno volumetriche. I passaggi per esportare i dati morfologici ed eseguire gruppo indipendente analisi basate su metriche morfologiche misurati per ogni neurone sono delineati. Ci sono limitazioni per metodi di clustering e ci sono anche una varietà di diversi algoritmi di clustering disponibili. Di conseguenza, sono descritte le opzioni ei vantaggi di alcuni degli algoritmi più comunemente usato. L&#39;analisi dei cluster non prevede la verifica statistica della unicità dei cluster. Pertanto, passaggi aggiuntivi sono delineati verificare raggruppamento ottimale nonché le relazioni tra i dati morfologici all&#39;interno e tra cluster. Metodi statistici per la valutazione cluster per il set di dati TRN per confermare che i neuroni TRN sono raggruppati in tre gruppi unici basato su 10 parametri morfologici indipendenti sono descritte. Così, delineando passi per selettivamente l&#39;etichettatura, Ricostruendo, e l&#39;analisi dei dati morfologici da una specifica popolazione neuronale, si descrivono i metodi per quantificare le differenze morfologiche tra i neuroni all&#39;interno di una popolazione. risultati precedenti di tipi neuronali distinti all&#39;interno del settore visivo del TRN scimmia macaco sono confermate con separati metodi di valutazione statistica. Insieme, ci auguriamo che queste tecniche saranno ampiamente applicabile a set di dati neuroanatomiche e aiutare a stabilire la classificazione quantitativa della diversità delle popolazioni neuronali attraverso il cervello.

<table><tbody><tr><td>SAD&amp;Delta;G-EGFP</td><td>E.M. Callaway Laboratory, Salk Institute</td><td></td><td>Prepared by Dr. F. Osakada. G-deleted rabies virus available through the Salk Institute Viral Core</td></tr><tr><td>Recording electrode: platinum/iridium or tungsten</td><td>FHC</td><td>UEPSGGSE1N2M</td><td>Visit website (www.fh-co.com) for alternative order specifications</td></tr><tr><td>Nanoject II</td><td>Drummod Scientific</td><td>3-000-204, 110V</td><td>Alternatives: picospritzer, Hamilton syringe</td></tr><tr><td>Freezing microtome</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>DAB</td><td>Sigma Aldrich</td><td>D5905-50TAB</td><td>3,3&#039;-Diaminobenzidine tetrahydrochloride, tablet, 10 mg substrate per tablet. Caution: carcinogen - must be bleached before discarding</td></tr><tr><td>Cytochrome C</td><td>Sigma Aldrich</td><td>C2037-100MG</td><td></td></tr><tr><td>Catalase</td><td>Sigma-Aldich</td><td>C9322-5G</td><td></td></tr><tr><td>Rabbit anti-GFP</td><td>Life Technologies/Thermo Fisher</td><td>#A-11122&amp;nbsp;</td><td>Primary antibody</td></tr><tr><td>Biotinylated goat anti-rabbit</td><td>Vector Laboratories</td><td>#BA-1000</td><td>Secondary antibody</td></tr><tr><td>Neurolucida System&amp;nbsp;</td><td>MicroBrightField</td><td></td><td>Software for neuron tracing and analysis. http://www.mbfbioscience.com/neurolucida</td></tr><tr><td>Neurolucida Explorer</td><td>MicroBrightField</td><td></td><td>Data export software</td></tr><tr><td>Microfire Camera&amp;nbsp;</td><td>Optronics</td><td></td><td>2-Megapixel true color microscope camera. http://www.simicroscopes.com/pdfs/microfire.pdf</td></tr><tr><td>Nikon E800 Microscope</td><td>Nikon Instruments Inc.</td><td></td><td>Biological research microscope. http://www.microscopyu.com/museum/eclipseE800.html</td></tr><tr><td>Matlab</td><td>The MathWorks Inc.&amp;nbsp;</td><td></td><td>Matrix-based computational mathematics software. http://www.mathworks.com</td></tr><tr><td>Microsoft Office Excel</td><td>Microsoft</td><td></td><td>Spreadsheet program</td></tr></tbody></table>

large-scale reconstructions and independent, unbiased clustering based on morphological metrics to classify neurons in selective populations

Questo protocollo delinea le ricostruzioni su larga scala di neuroni in combinazione con l&#39;uso di cluster indipendente e imparziale analisi per creare un&#39;indagine completa delle caratteristiche morfologiche osservate in una popolazione neuronale selettiva. La combinazione di queste tecniche costituisce un nuovo approccio per la raccolta e l&#39;analisi dei dati neuroanatomici. Insieme, queste tecniche consentono di larga scala, e quindi più completo, il campionamento delle popolazioni neuronali selettivi e stabilire metodi quantitativi per la descrizione imparziali classi neuronali morfologicamente unici all&#39;interno di una popolazione. Il protocollo descrive l&#39;uso di virus della rabbia modificato per etichettare selettivamente i neuroni. G-cancellato atti virus della rabbia come tracciante retrogrado seguenti iniezione stereotassica in una struttura di destinazione cerebrale di interesse e serve come veicolo per l&#39;erogazione e l&#39;espressione di EGFP in neuroni. Un gran numero di neuroni sono infettate con questotecnica e di esprimere la GFP per tutta la loro dendriti, la produzione di &quot;Golgi-like&quot; riempimenti completi dei singoli neuroni. Di conseguenza, il metodo di analisi retrograda virus-mediata migliora le tecniche di tracciamento retrogrado tradizionali a base di coloranti con la produzione di riempimenti intracellulari completi. I singoli neuroni ben isolate che abbracciano tutte le regioni della zona del cervello in fase di studio sono selezionati per la ricostruzione al fine di ottenere un campione rappresentativo di neuroni. Il protocollo delinea le procedure per ricostruire corpi cellulari e completare i modelli arborizzazione dendritiche di neuroni marcati che abbracciano molteplici sezioni di tessuto. dati morfologici, comprese le posizioni di ogni neurone all&#39;interno della struttura del cervello, vengono estratti per ulteriori analisi. funzioni di programmazione standard sono stati utilizzati per eseguire gruppo indipendente analisi e valutazioni cluster basato su metriche morfologiche. Per verificare l&#39;utilità di queste analisi, valutazione statistica di un perfo cluster analysisconfermate su 160 neuroni ricostruite nel nucleo reticolare del talamo del talamo (TRN) del macaco è stato fatto. Sia la cluster analysis originale e le valutazioni statistiche svolte qui indicano che i neuroni TRN sono separati in tre sottopopolazioni, ognuno con caratteristiche morfologiche uniche.

Abbiamo dimostrato in precedenza che le ricostruzioni su larga scala di neuroni all&#39;interno di una popolazione selettivo sta seguendo iniezione fattibile del virus della rabbia modificato nel dLGN 5. Recentemente, lo stesso tessuto è stato utilizzato per ricostruire 160 neuroni nel settore visivo del TRN (Bragg et al, in revisione;. Figure 2A-B) seguendo le fasi metodologiche dettagliate qui sopra descritti. Nello studio TRN, tre gruppi ...

Watch this Scientific Journal Video about Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations at JoVE.com

Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations

Questo protocollo descrive ricostruzioni su larga scala di popolazioni neuronali selettivi, etichettati dopo l&#39;infezione retrograda con esprimendo un virus della rabbia modificato marcatori fluorescenti, e le analisi di cluster indipendente, imparziale che consentono la caratterizzazione completa delle metriche morfologiche tra sottoclassi neuronali distinti.

Ricostruzioni su larga scala e indipendente, imparziale Clustering Sulla base morfologici metrica per classificare i neuroni in selettivi Popolazioni

This protocol outlines large-scale reconstructions of neurons combined with the use of independent and unbiased clustering analyses to create a ...

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Research

JoVE Journal

Neuroscience

6.9K Views.  Geisel School of Medicine at Dartmouth.  Questo protocollo descrive ricostruzioni su larga scala di popolazioni neuronali selettivi, etichettati dopo l'infezione retrograda con esprimendo un virus della rabbia modificato marcatori fluorescenti, e le analisi di cluster indipendente, imparziale che consentono la caratterizzazione completa delle metriche morfologiche tra sottoclassi neuronali distinti. 

Video: Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations

Automated Sholl Analysis of Digitized Neuronal Morphology at Multiple Scales

Neuronal morphology plays a significant role in determining how neurons function and communicate1-3. Specifically, it affects the ability of neurons to receive inputs from other cells2 and contributes to the propagation of action potentials4,5. The morphology of the neurites also affects how information is processed. The diversity of dendrite morphologies facilitate local and long range signaling and allow individual neurons or groups of neurons to carry out specialized functions within the neuronal network6,7. Alterations in dendrite morphology, including fragmentation of dendrites and changes in branching patterns, have been observed in a number of disease states, including Alzheimer's disease8, schizophrenia9,10, and mental retardation11. The ability to both understand the factors that shape dendrite morphologies and to identify changes in dendrite morphologies is essential in the understanding of nervous system function and dysfunction.
Neurite morphology is often analyzed by Sholl analysis and by counting the number of neurites and the number of branch tips. This analysis is generally applied to dendrites, but it can also be applied to axons. Performing this analysis by hand is both time consuming and inevitably introduces variability due to experimenter bias and inconsistency. The Bonfire program is a semi-automated approach to the analysis of dendrite and axon morphology that builds upon available open-source morphological analysis tools. Our program enables the detection of local changes in dendrite and axon branching behaviors by performing Sholl analysis on subregions of the neuritic arbor. For example, Sholl analysis is performed on both the neuron as a whole as well as on each subset of processes (primary, secondary, terminal, root, etc.) Dendrite and axon patterning is influenced by a number of intracellular and extracellular factors, many acting locally. Thus, the resulting arbor morphology is a result of specific processes acting on specific neurites, making it necessary to perform morphological analysis on a smaller scale in order to observe these local variations12.
The Bonfire program requires the use of two open-source analysis tools, the NeuronJ plugin to ImageJ and NeuronStudio. Neurons are traced in ImageJ, and NeuronStudio is used to define the connectivity between neurites. Bonfire contains a number of custom scripts written in MATLAB (MathWorks) that are used to convert the data into the appropriate format for further analysis, check for user errors, and ultimately perform Sholl analysis. Finally, data are exported into Excel for statistical analysis. A flow chart of the Bonfire program is shown in Figure 1.

We have developed a computer program to analyze neuronal morphology. In combination with two existing open source analysis tools, our program performs Sholl analysis and determines the number of neurites, branch points, and neurite tips. The analyses are performed so that local changes in neurite morphology can be observed.

Analisi automatizzata Sholl di Digitized morfologia neuronale a scale multiple

Neuronal morphology plays a significant role in determining how neurons function and communicate1-3.  Specifically, it affects the ability of neurons to ...

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Neuroscienze

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

The appearance and the movements of immune cells are driven by their environment. As a reaction to a pathogen invasion, the immune cells are recruited to the site of inflammation and are activated to prevent a further spreading of the invasion. This is also reflected by changes in the behavior and the morphological appearance of the immune cells. In cancerous tissue, similar morphokinetic changes have been observed in the behavior of microglial cells: intra-tumoral microglia have less complex 3-dimensional shapes, having less-branched cellular processes, and move more rapidly than those in healthy tissue. The examination of such morphokinetic properties requires complex 3D microscopy techniques, which can be extremely challenging when executed longitudinally. Therefore, the recording of a static 3D shape of a cell is much simpler, because this does not require intravital measurements and can be performed on excised tissue as well. However, it is essential to possess analysis tools that allow the fast and precise description of the 3D shapes and allows the diagnostic classification of healthy and pathogenic tissue samples based solely on static, shape-related information. Here, we present a toolkit that analyzes the discrete Fourier components of the outline of a set of 2D projections of the 3D cell surfaces via Self-Organizing Maps. The application of artificial intelligence methods allows our framework to learn about various cell shapes as it is applied to more and more tissue samples, whilst the workflow remains simple.

Here, we provide a workflow that allows the identification of healthy and pathological cells based on their 3-dimensional shape. We describe the process of using 2D projection outlines based on the 3D surfaces to train a Self-Organizing Map that will provide objective clustering of the investigated cell populations.

Basato su morfologia distinzione tra sano e patologico delle cellule utilizzando trasformazioni di Fourier e Self-Organizing Maps

The appearance and the movements of immune cells are driven by their environment. As a reaction to a pathogen invasion, the immune cells are recruited to ...

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Electrophysiological and Morphological Characterization of Neuronal Microcircuits in Acute Brain Slices Using Paired Patch-Clamp Recordings

The combination of patch clamp recordings from two (or more) synaptically coupled neurons (paired recordings) in acute brain slice preparations with simultaneous intracellular biocytin filling allows a correlated analysis of their structural and functional properties. With this method it is possible to identify and characterize both pre- and postsynaptic neurons by their morphology and electrophysiological response pattern. Paired recordings allow studying the connectivity patterns between these neurons as well as the properties of both chemical and electrical synaptic transmission. Here, we give a step-by-step description of the procedures required to obtain reliable paired recordings together with an optimal recovery of the neuron morphology. We will describe how pairs of neurons connected via chemical synapses or gap junctions are identified in brain slice preparations. We will outline how neurons are reconstructed to obtain their 3D morphology of the dendritic and axonal domain and how synaptic contacts are identified and localized. We will also discuss the caveats and limitations of the paired recording technique, in particular those associated with dendritic and axonal truncations during the preparation of brain slices because these strongly affect connectivity estimates. However, because of the versatility of the paired recording approach it will remain a valuable tool in characterizing different aspects of synaptic transmission at identified neuronal microcircuits in the brain.

Patch-clamp recordings and simultaneous intracellular biocytin filling of synaptically coupled neurons in acute brain slices allow a correlated analysis of their structural and functional properties. The aim of this protocol is to describe the essential technical steps of electrophysiological recording from neuronal microcircuits and their subsequent morphological analysis.

Elettrofisiologici e morfologica Caratterizzazione neuronali Microcircuiti in Acute Fette cervello Utilizzando accoppiati di patch-clamp Recordings

The combination of patch clamp recordings from two (or more) synaptically coupled neurons (paired recordings) in acute brain slice preparations with ...

Analyzing Dendritic Morphology in Columns and Layers

In many regions of the central nervous systems, such as the fly optic lobes and the vertebrate cortex, synaptic circuits are organized in layers and columns to facilitate brain wiring during development and information processing in developed animals. Postsynaptic neurons elaborate dendrites in type-specific patterns in specific layers to synapse with appropriate presynaptic terminals. The fly medulla neuropil is composed of 10 layers and about 750 columns; each column is innervated by dendrites of over 38 types of medulla neurons, which match with the axonal terminals of some 7 types of afferents in a type-specific fashion. This report details the procedures to image and analyze dendrites of medulla neurons. The workflow includes three sections: (i) the dual-view imaging section combines two confocal image stacks collected at orthogonal orientations into a high-resolution 3D image of dendrites; (ii) the dendrite tracing and registration section traces dendritic arbors in 3D and registers dendritic traces to the reference column array; (iii) the dendritic analysis section analyzes dendritic patterns with respect to columns and layers, including layer-specific termination and planar projection direction of dendritic arbors, and derives estimates of dendritic branching and termination frequencies. The protocols utilize custom plugins built on the open-source MIPAV (Medical Imaging Processing, Analysis, and Visualization) platform and custom toolboxes in the matrix laboratory language. Together, these protocols provide a complete workflow to analyze the dendritic routing of Drosophila medulla neurons in layers and columns, to identify cell types, and to determine defects in mutants.

Here, we show how to analyze dendritic routing of Drosophila medulla neurons in columns and layers. The workflow includes a dual-view imaging technique to improve the image quality and computational tools for tracing, registering dendritic arbors to the reference column array and for analyzing the dendritic structures in 3D space.

Analizzando dendritiche Morfologia in colonne e strati

In many regions of the central nervous systems, such as the fly optic lobes and the vertebrate cortex, synaptic circuits are organized in layers and ...

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical properties, synaptic connections, and in vivo functions, but their basic functional and anatomical organization from cellular to network scale is poorly understood. Here we describe a method for the three-dimensional imaging of fluorescently-labeled neurons across large areas of the brain for the investigation of the cortical cellular organization. Specific types of neurons are labeled by the injection of fluorescent retrograde neuronal tracers or expression of fluorescent proteins in transgenic mice. Block brain samples, e.g., a hemisphere, are prepared after fixation, made transparent with tissue clearing methods, and subjected to fluorescent immunolabeling of the specific cell types. Large areas are scanned using confocal or two-photon microscopes equipped with large working distance objectives and motorized stages. This method can resolve the periodic organization of the cell type-specific microcolumn functional modules in the mouse neocortex. The procedure can be useful for the study of three-dimensional cellular architecture in the diverse brain areas and other complex tissues.

Here we describe a procedure for tissue clearing, fluorescent labeling, and large-scale imaging of mouse brain tissue which, thereby, enables visualization of the three-dimensional organization of cell types in the neocortex.

Formazione immagine tridimensionale su larga scala di organizzazione cellulare nella neocorteccia Mouse

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical ...

Biocytin Recovery and 3D Reconstructions of Filled Hippocampal CA2 Interneurons

How cortical network activity processes information is of importance to a large number of basic and clinical scientific questions. The protocol described here identifies the basic building blocks of this circuitry. The in-depth studies of cortical regions will ultimately provide other scientists with the circuit components needed for an understanding of how the brain acquires, processes and stores information and what goes wrong in disease, while the electrophysiological and morphological data are widely used by computational neuroscientists in the construction of model networks that explore information processing. The protocol outlined here describes how biocytin-filled cells recorded in the CA2 region of the hippocampus are recovered and then reconstructed in&#160;3D. Additionally, the protocol describes the demonstration of calcium binding protein or peptide content in recorded interneurons.

The protocol outlined here describes the immunofluorescence analysis, biocytin recovery and high-quality reconstructions of hippocampal CA2 interneurons following the intracellular electrophysiological recordings in vitro, allowing neuronal characterization and ultimately fine neuronal anatomy to be studied.

Recupero di biocitina e ricostruzioni 3D di interneuroni riempito Hippocampal CA2

How cortical network activity processes information is of importance to a large number of basic and clinical scientific questions. The protocol described ...

A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells

Serial sectioning and subsequent high-resolution imaging of biological tissue using electron microscopy (EM) allow for the segmentation and reconstruction of high-resolution imaged stacks to reveal ultrastructural patterns that could not be resolved using 2D images. Indeed, the latter might lead to a misinterpretation of morphologies, like in the case of mitochondria; the use of 3D models is, therefore, more and more common and applied to the formulation of morphology-based functional hypotheses. To date, the use of 3D models generated from light or electron image stacks makes qualitative, visual assessments, as well as quantification, more convenient to be performed directly in 3D. As these models are often extremely complex, a virtual reality environment is also important to be set up to overcome occlusion and to take full advantage of the 3D structure. Here, a step-by-step guide from image segmentation to reconstruction and analysis is described in detail.

The described pipeline is designed for the segmentation of electron microscopy datasets larger than gigabytes, to extract whole-cell morphologies. Once the cells are reconstructed in 3D, customized software designed around individual needs can be used to perform a qualitative and quantitative analysis directly in 3D, also using virtual reality to overcome view occlusion.

Un metodo per la ricostruzione 3D e l'analisi della realtà virtuale delle cellule gliali e neuronali

Serial sectioning and subsequent high-resolution imaging of biological tissue using electron microscopy (EM) allow for the segmentation and reconstruction ...

Ballistic Labeling of Pyramidal Neurons in Brain Slices and in Primary Cell Culture

It has been reported that the size and shape of dendritic spines is related to their structural plasticity. To identify the morphological structure of pyramidal neurons and dendritic spines, a ballistic labeling technique can be utilized. In the present protocol, pyramidal neurons are labeled with DilC18(3) dye and analyzed using neuronal reconstruction software to assess neuronal morphology and dendritic spines. To investigate neuronal structure, dendritic branching analysis and Sholl analysis are performed, allowing researchers to draw inferences about dendritic branching complexity and neuronal arbor complexity, respectively. The evaluation of dendritic spines is conducted using an automatic assisted classification algorithm integral to the reconstruction software, which classifies spines into four categories (i.e., thin, mushroom, stubby, filopodia). Furthermore, an additional three parameters (i.e., length, head diameter, and volume) are also chosen to assess alterations in dendritic spine morphology. To validate the potential of wide application of the ballistic labeling technique, pyramidal neurons from in vitro cell culture were successfully labeled. Overall, the ballistic labeling method is unique and useful for visualizing neurons in different brain regions in rats, which in combination with sophisticated reconstruction software, allows researchers to elucidate the possible mechanisms underlying neurocognitive dysfunction.

We present a protocol to label and analyze pyramidal neurons, which is critical for evaluating potential morphological alterations in neurons and dendritic spines that may underlie neurochemical and behavioral abnormalities.

Etichettatura balistica dei neuroni piramidali nelle sezioni cerebrali e nella cultura cellulare primaria

It has been reported that the size and shape of dendritic spines is related to their structural plasticity. To identify the morphological structure of ...

Automatic Identification of Dendritic Branches and their Orientation

The structure of neuronal dendritic trees plays a key role in the integration of synaptic inputs in neurons. Therefore, characterization of the morphology of dendrites is essential for a better understanding of neuronal function. However, the complexity of dendritic trees, both when isolated and especially when located within neuronal networks, has not been completely understood. We developed a new computational tool, SOA (Segmentation and Orientation Analysis), which allows automatic measurement of the orientation of dendritic branches from fluorescence images of 2D neuronal cultures. SOA, written in Python, uses segmentation to distinguish dendritic branches from the image background and accumulates a database on the spatial direction of each branch. The database is then used to calculate morphological parameters such as the directional distribution of dendritic branches in a network and the prevalence of parallel dendritic branch growth. The data obtained can be used to detect structural changes in dendrites in response to neuronal activity and to biological and pharmacological stimuli.

Presented is a computational tool that allows simple and direct automatic measurement of orientations of neuronal dendritic branches from 2D fluorescence images.

Identificazione automatica dei rami dendritici e loro orientamento

The structure of neuronal dendritic trees plays a key role in the integration of synaptic inputs in neurons. Therefore, characterization of the morphology ...

A Tissue Clearing Method for Neuronal Imaging from Mesoscopic to Microscopic Scales

A detailed protocol is provided here to visualize neuronal structures from mesoscopic to microscopic levels in brain tissues. Neuronal structures ranging from neural circuits to subcellular neuronal structures are visualized in mouse brain slices optically cleared with ScaleSF. This clearing method is a modified version of ScaleS and is a hydrophilic tissue clearing method for tissue slices that achieves potent clearing capability as well as a high-level of preservation of fluorescence signals and structural integrity. A customizable three dimensional (3D)-printed imaging chamber is designed for reliable mounting of cleared brain tissues. Mouse brains injected with an adeno-associated virus vector carrying enhanced green fluorescent protein gene were fixed with 4% paraformaldehyde and cut into slices of 1-mm thickness with a vibrating tissue slicer. The brain slices were cleared by following the clearing protocol, which include sequential incubations in three solutions, namely, ScaleS0 solution, phosphate buffer saline (&#8211;), and ScaleS4 solution, for a total of 10.5&#8211;14.5 h. The cleared brain slices were mounted on the imaging chamber and embedded in 1.5% agarose gel dissolved in ScaleS4D25(0) solution. The 3D image acquisition of the slices was carried out using a confocal laser scanning microscope equipped with a multi-immersion objective lens of a long working distance. Beginning with mesoscopic neuronal imaging, we succeeded in visualizing fine subcellular neuronal structures, such as dendritic spines and axonal boutons, in the optically cleared brain slices. This protocol would facilitate understanding of neuronal structures from circuit to subcellular component scales.

The protocol provides a detailed method of neuronal imaging in brain slice using a tissue clearing method, ScaleSF. The protocol includes brain tissue preparation, tissue clarification, handling of cleared slices and confocal laser scanning microscopy imaging of neuronal structures from mesoscopic to microscopic levels.

Un metodo di compensazione dei tessuti per l'imaging neuronale dalle scale mesoscopiche a quelle microscopiche

A detailed protocol is provided here to visualize neuronal structures from mesoscopic to microscopic levels in brain tissues. Neuronal structures ranging ...