“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone

Abstract The subventricular zone (SVZ) is a region of ongoing postnatal germinal activity that shows complex spatial heterogeneity. For instance, different SVZ microdomains contain neural stem cells that express distinct transcription factors and generate different glial and neuronal progenies. Thes...

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Autores principales:	Stefan Zweifel, Julie Buquet, Lorenzo Caruso, David Rousseau, Olivier Raineteau
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	FlashMap Subventricular Zone (SVZ) Germinal Activity Germinal Regions Heatmap Medicine R Science Q
Acceso en línea:	https://doaj.org/article/55a332486bb64edfb780c6753d510a09
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spelling	oai:doaj.org-article:55a332486bb64edfb780c6753d510a092021-12-02T15:08:51Z“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone10.1038/s41598-018-33939-12045-2322https://doaj.org/article/55a332486bb64edfb780c6753d510a092018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-33939-1https://doaj.org/toc/2045-2322Abstract The subventricular zone (SVZ) is a region of ongoing postnatal germinal activity that shows complex spatial heterogeneity. For instance, different SVZ microdomains contain neural stem cells that express distinct transcription factors and generate different glial and neuronal progenies. These unique characteristics call for the development of new methods to integrate a spatial dimension to histological analyses performed in this germinal region. We developed “FlashMap”, a semi-automatic software that allows the segmentation and rapid measurement of optical densities throughout the full SVZ coordinates. “FlashMap” generates easily readable two-dimensional heatmaps that can be superimposed onto three-dimensional reconstructions of the ventricular system for optimal spatial exploration. Accurate heatmaps can be obtained, even following serial section subsampling thereby reducing the amount of tissue and time required for histological analysis. We first illustrate the potential of “FlashMap” by spatially exploring the correlation of SVZ thickness and cellular density with germinal activity throughout its rostro-caudal coordinates. We then used “FlashMap” to analyse the spatial expression of the transcription factors Dlx2, Tbr2 and Hopx as well as of the immature neuronal marker Dcx, to demonstrate the suitability of this approach to explore the regional production of cells of distinct lineages by defined SVZ microdomains.Stefan ZweifelJulie BuquetLorenzo CarusoDavid RousseauOlivier RaineteauNature PortfolioarticleFlashMapSubventricular Zone (SVZ)Germinal ActivityGerminal RegionsHeatmapMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-13 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	FlashMap Subventricular Zone (SVZ) Germinal Activity Germinal Regions Heatmap Medicine R Science Q
spellingShingle	FlashMap Subventricular Zone (SVZ) Germinal Activity Germinal Regions Heatmap Medicine R Science Q Stefan Zweifel Julie Buquet Lorenzo Caruso David Rousseau Olivier Raineteau “FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone
description	Abstract The subventricular zone (SVZ) is a region of ongoing postnatal germinal activity that shows complex spatial heterogeneity. For instance, different SVZ microdomains contain neural stem cells that express distinct transcription factors and generate different glial and neuronal progenies. These unique characteristics call for the development of new methods to integrate a spatial dimension to histological analyses performed in this germinal region. We developed “FlashMap”, a semi-automatic software that allows the segmentation and rapid measurement of optical densities throughout the full SVZ coordinates. “FlashMap” generates easily readable two-dimensional heatmaps that can be superimposed onto three-dimensional reconstructions of the ventricular system for optimal spatial exploration. Accurate heatmaps can be obtained, even following serial section subsampling thereby reducing the amount of tissue and time required for histological analysis. We first illustrate the potential of “FlashMap” by spatially exploring the correlation of SVZ thickness and cellular density with germinal activity throughout its rostro-caudal coordinates. We then used “FlashMap” to analyse the spatial expression of the transcription factors Dlx2, Tbr2 and Hopx as well as of the immature neuronal marker Dcx, to demonstrate the suitability of this approach to explore the regional production of cells of distinct lineages by defined SVZ microdomains.
format	article
author	Stefan Zweifel Julie Buquet Lorenzo Caruso David Rousseau Olivier Raineteau
author_facet	Stefan Zweifel Julie Buquet Lorenzo Caruso David Rousseau Olivier Raineteau
author_sort	Stefan Zweifel
title	“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone
title_short	“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone
title_full	“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone
title_fullStr	“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone
title_full_unstemmed	“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone
title_sort	“flashmap” - a semi-automatic tool for rapid and accurate spatial analysis of marker expression in the subventricular zone
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/55a332486bb64edfb780c6753d510a09
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“FlashMap” - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone

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