Name: clock scan protocol for image analysis: imagej plugins
Uploaded: 2017-06-19T13:00:00
Description: Watch this Scientific Journal Video about Clock Scan Protocol for Image Analysis: ImageJ Plugins at JoVE.com

我们感谢Tanja Maritzen博士和Fabian Feutlinske博士（莱布尼兹德国柏林分子药理学研究所）与我们分享了他们的Fuji ImageJ Clock Scan插件版本，并激励我们开发此版本的程序。我们也非常感谢弗里茨·梅尔切斯博士（Max Planck感染生物学研究所淋巴细胞发育系）对他部门的数据库使用图像进行测试和改进插件的许可。支持：翻译神经科学中心; NIH授权：P30-GM110702-03。

软件安装<ol><li>按照相应网站的推荐安装最新版本的捆绑Java和ImageJ或Fiji ImageJ（请参阅材料表，以获取相应网站的链接）。在下面的文本中，这两个程序都被称为“ImageJ”。 </li><li>使用材料表中提供的链接复制“Clock_Scan-1.0.1。jar”和“Multi_Clock_Scan-1.0.1.jar”插件文件，并将其粘贴到ImageJ插件目录中。或者，使用“插件|安装插件”菜单选项将它们保存在计算机硬盘驱动器上之后安装这些文件。 </l...

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	<li>Dobretsov, M., Romanovsky, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="Clock-scan"+protocol+for+image+analysis.">"Clock-scan" protocol for image analysis.</a> Am J Physiol Cell Physiol. 291, 869-879 (2006).</li><li>Feutlinske, F., Browarski, M., Ku, M. C., 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=Stonin1+mediates+endocytosis+of+the+proteoglycan+NG2+and+regulates+focal+adhesion+dynamics+and+cell+motility.">Stonin1 mediates endocytosis of the proteoglycan NG2 and regulates focal adhesion dynamics and cell motility.</a> Nat Commun. 6, 8535 (2015).</li><li>Schneider, C. A., Rasband, W. S., Eliceiri, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NIH+Image+to+ImageJ:+25+years+of+image+analysis.">NIH Image to ImageJ: 25 years of image analysis.</a> Nat Methods. 9, 671-675 (2012).</li><li>Schindelin, J., Arganda-Carreras, I., Frise, E., 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=Fiji:+an+open-source+platform+for+biological-image+analysis.">Fiji: an open-source platform for biological-image analysis.</a> Nat Methods. 9, 676-682 (2012).</li><li>Dobretsov, M., Hastings, S. L., Stimers, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Non-uniform+expression+of+alpha+subunit+isoforms+of+the+Na+/K++pump+in+rat+dorsal+root+ganglia+neurons.">Non-uniform expression of alpha subunit isoforms of the Na+/K+ pump in rat dorsal root ganglia neurons.</a> Brain Res. 821, 212-217 (1999).</li><li>Hayar, A., Gu, C., Al-Chaer, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+improved+method+for+patch+clamp+recording+and+calcium+imaging+of+neurons+in+the+intact+dorsal+root+ganglion+in+rats.">An improved method for patch clamp recording and calcium imaging of neurons in the intact dorsal root ganglion in rats.</a> J Neurosci Methods. 173, 74-82 (2008).</li><li>Dobretsov, M., Pierce, D., Light, K. E., Kockara, N. T., Kozhemyakin, M., Wight, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transgenic+mouse+model+to+selectively+identify+alpha3+Na,K-ATPase+expressing+cells+in+the+nervous+system.">Transgenic mouse model to selectively identify alpha3 Na,K-ATPase expressing cells in the nervous system.</a> Society for Neuroscience. , 1 (2015).</li><li>Lein, E. S., Hawrylycz, M. J., Ao, N., 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=Genome-wide+atlas+of+gene+expression+in+the+adult+mouse+brain.">Genome-wide atlas of gene expression in the adult mouse brain.</a> Nature. 445, 168-176 (2007).</li><li>Romanovsky, D., Mrak, R. E., Dobretsov, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Age-dependent+decline+in+density+of+human+nerve+and+spinal+ganglia+neurons+expressing+the+alpha3+isoform+of+Na/K-ATPase.">Age-dependent decline in density of human nerve and spinal ganglia neurons expressing the alpha3 isoform of Na/K-ATPase.</a> Neuroscience. 310, 342-353 (2015).</li><li>Campbell, J., Singh, D., Hollett, G., 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=Spatially+selective+photoconductive+stimulation+of+live+neurons.">Spatially selective photoconductive stimulation of live neurons.</a> Front Cell Neurosci. 8, 142 (2014).</li><li>Yuryev, M., Pellegrino, C., Jokinen, V., 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=In+vivo+Calcium+Imaging+of+Evoked+Calcium+Waves+in+the+Embryonic+Cortex.">In vivo Calcium Imaging of Evoked Calcium Waves in the Embryonic Cortex.</a> Front Cell Neurosci. 9, 500 (2015).</li><li>Qiao, M., Sanes, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+Method+for+Labeling+Electrically+Coupled+Cells:+Application+to+Retina.">Genetic Method for Labeling Electrically Coupled Cells: Application to Retina.</a> Front Mol Neurosci. 8, 81 (2015).</li></ol>

时钟扫描协议：时钟扫描协议是一种快速简单的图像分析工具。与现有的图像分析方法（例如线性像素强度扫描或ROI的平均像素强度的计算）相比，该协议的优点已经在先前的出版物1,9中进行了详细描述。简而言之，该协议允许通过量化位于与ROI中心不同距离（例如对象的边界）或物体外部的预定位置（背景）的像素的强度来生成整体的径向像素强度分布。由于后者，每个ROI的时钟?...

这项工作的目标是提供一个无平台的时钟扫描协议，并可免费向任何对这种图像分析感兴趣的研究人员提供。时钟扫描协议最初是在2006年开发的，目的是改进现有的凸型感兴趣区域（ROI）中的像素强度量化方法，一种具有更好的综合能力和改进的空间分辨率的方法。在采集期间，为了测量“背景”像素强度，协议顺序地收集从ROI中心扫描到其边界或ROI外的预定距离的多个径向像素强度分布。协议根据扫描方向测量的单元格半径来缩放这些轮廓。因此，从每个单独径向扫描的中心到ROI边界的距离总是X刻度的100％。最后，程序平均这些个人al轮廓成一个整体的径向像素强度分布。由于缩放，由“时钟扫描”协议产生的平均像素强度分布不依赖于ROI大小，也不在合理的限度内取决于ROI形状。该方法允许直接比较，或者如果需要，可以平均或减去不同ROI的配置文件。该协议还允许通过简单减去位于对象外部的像素的平均强度来校正任何对象的背景噪声的整体像素强度分布。虽然它只在生物样品中进行了测试，但是我们的协议为其他现有的图像分析工具提供了有价值的补充，这些工具用于研究物理或化学过程的图像，这些图像分布在原点附近（如从点源扩散物质） 1 。 然而，原始图像分析方法的主要限制是协议是dev作为Visual Basic 6（VB6）（代码，因此它依赖于平台，难以分发（需要VB6）。为了解决这个问题，并加入了其他调查人员近期的类似工作，我们转换了VB6时钟扫描程序代码转换为两个基于Java的插件，与NIH赞助和免费提供的开源和平台无关的图像分析程序ImageJ 3和Fiji ImageJ 4兼容，此外，这些插件现在有几个新功能可扩展功能的原始协议来处理多个ROI和图像堆栈许多图像分析应用程序不是用户友好的，关于对多个对象进行统计分析，因此通常只显示代表性的数据。通过多时钟扫描ImageJ插件，可以同时促进多个物体的分析，对显微镜数据的鲁棒统计评估，关于单个单元/对象中的信号强度分布，现在可以通过该插件扩展。在这里，我们将描述时钟扫描插件，并在图像分析中显示其应用的示例。

<table border="0" cellpadding="0" cellspacing="0" width="896">
	<colgroup>
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		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Computer</td>
			<td style="width:71px;">Any</td>
			<td style="width:289px;"></td>
			<td style="width:320px;">compatible with software listed below</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ImageJ or Fiji ImageJ</td>
			<td style="width:71px;">NIH</td>
			<td>https://imagej.nih.gov/ij/ or https://fiji.sc/</td>
			<td>bundled with Java 1.8 or higher</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Clock-scan plugins</td>
			<td style="width:71px;">freeware</td>
			<td>https://sourceforge.net/projects/clockscan/</td>
			<td>Clock_Scan-1.0.1 jar and Multi_Clock_Scan-1.0.1/ jar</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">Origin 9.0</td>
			<td>OriginLab</td>
			<td style="width:289px;">Northampton, MA, USA</td>
			<td style="width:320px;">This program was used to generate some graphs of the original Clock Scan data. Any other graphic software can be used to perform this function</td>
		</tr>
	</tbody>
</table>

clock scan protocol for image analysis: imagej plugins

用于图像分析的时钟扫描协议是量化在边界内部和外部（背景）在关闭或分段的凸起的感兴趣区域内的平均像素强度的有效工具，导致产生平均的整体径向像素 - 强度分布。该协议最初是在2006年开发的，作为一个视觉基本的6脚本，但是它的分布有限。为了解决这个问题，并加入其他人近期的类似工作，我们将原始的时钟扫描协议代码转换为与NIH赞助和免费提供的图像分析程序（如ImageJ或Fiji ImageJ）兼容的两个基于Java的插件。此外，这些插件具有几个新功能，进一步扩展了原始协议的功能范围，如分析多个感兴趣区域和图像堆栈。程序的后一个特征在确定相关变更很重要的应用中特别有用到时间和位置。因此，生物图像堆叠的时钟扫描分析可能潜在地应用于单个细胞内Na +或Ca ++的扩散，以及对突触群体中扩散活性（ 例如 ，Ca ++波）的分析连接或间隙结耦合电池。在这里，我们将描述这些新的时钟扫描插件，并在图像分析中展示其应用的一些示例。

这里用于说明目的的图像取自我们之前的细胞和组织生物学研究5,6,7和从Allen Mouse Brain Atlas 8中创建的数据库。这两个插件都使用ImageJ 1.50i / Java 1.8.0_77，ImageJ 2.0.0-rc-44 / 1.50e / Java 1.8.9_66和Fiji ImageJ 2.0.0-rc54 / 1.51g / Java 1.8.0_66程序环境成功测试。 图1显示了使用标准时钟扫?...

Watch this Scientific Journal Video about Clock Scan Protocol for Image Analysis: ImageJ Plugins at JoVE.com

Clock Scan Protocol for Image Analysis: ImageJ Plugins

本文介绍了用于“时钟扫描”图像分析的两个新颖的ImageJ插件。这些插件扩展了原始视觉基础6程序的功能，最重要的是，通过将其与ImageJ免费图像分析软件包捆绑在一起，使程序可用于大型研究团体。

用于图像分析的时钟扫描协议：ImageJ插件

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a ...

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