Name: measuring the shape and size of activated sludge particles immobilized in agar with an open source software pipeline
Uploaded: 2019-01-30T14:45:00
Description: Watch this Scientific Journal Video about Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline at JoVE.com

这项工作得到了国家科学基金会 cbet 1336544 的赠款的支持。
fiji、r 和 python 徽标与以下商标政策一起使用: python: <a href="https://www.python.org/psf/trademarks/">https://www.python.org/psf/trademarks/</a> r: <a href="https://www.r-project.org/logo/">https://www.r-project.org/Logo/</a> , 根据 cc-by-sa 4.0 许可证列于: <a href="https://creativecommons.org/licenses/by-sa/4.0/">https://creativecommons.org/Licenses/by-sa/4.0/</a> 斐济: <a href="https://imagej.net/Licensing">https://imagej.net/Licensing</a>

1. 收集样品进行颗粒分析
<ol><li>确定特定反应器的样品体积, 这些颗粒将产生足够的颗粒用于统计分析10 (& gt;500), 同时避免颗粒重叠。<ol>
<li>假设每个混合液样品的范围为0.5 至2毫升, 足以用于混合液悬浮固体 (mlss) 在250至 5, 000 mg/l 之间的活性污泥样品。</li>
		<li>否则, 请使用0.5、2和 5 ml 样品 (步骤1.2 至 2.7) 制备三个测试琼脂板。</li>
		<li>直观地估计哪些 (如果有) 样本量最符合?...

<ol>
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Effect of Hydrodynamics on Aerobic Granulation Available from: <a target="_blank" href="https://repository.lib.ncsu.edu/handle/1840.16/8761">https://repository.lib.ncsu.edu/handle/1840.16/8761</a> (2012)</li><li>Tay, J. H., Liu, Q. S., Liu, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microscopic+observation+of+aerobic+granulation+in+sequential+aerobic+sludge+blanket+reactor.">Microscopic observation of aerobic granulation in sequential aerobic sludge blanket reactor.</a> Journal of Applied Microbiology. 91 (1), 168-175 (2001).</li><li>Kelly, R. 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=Graphical+Comparison+of+Image+Analysis+and+Laser+Diffraction+Particle+Size+Analysis+Data+Obtained+From+the+Measurements+of+Nonspherical+Particle+Systems.">Graphical Comparison of Image Analysis and Laser Diffraction Particle Size Analysis Data Obtained From the Measurements of Nonspherical Particle Systems.</a> AAPS Pharm SciTech. 7 (3), E1-E14 (2006).</li><li>Walisko, R., 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=The+Taming+of+the+Shrew+-Controlling+the+Morphology+of+Filamentous+Eukaryotic+and+Prokaryotic+Microorganisms.">The Taming of the Shrew -Controlling the Morphology of Filamentous Eukaryotic and Prokaryotic Microorganisms.</a> Advances in Biochemical Engineering/Biotechnology. 149, 1-27 (2015).</li><li>Campbell, R. A. A., Eifert, R. W., Turner, G. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Openstage:+A+Low-Cost+Motorized+Microscope+Stage+with+Sub-Micron+Positioning+Accuracy.">Openstage: A Low-Cost Motorized Microscope Stage with Sub-Micron Positioning Accuracy.</a> PLoS ONE. 9 (2), e88977 (2014).</li><li>Dias, P. A., 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=Image+processing+for+identification+and+quantification+of+filamentous+bacteria+in+in+situ+acquired+images.">Image processing for identification and quantification of filamentous bacteria in in situ acquired images.</a> BioMedical Engineering OnLine. 15 (1), 64 (2016).</li><li>Liao, J., Lou, I., de los Reyes, F. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relationship+of+Species-Specific+Filament+Levels+to+Filamentous+Bulking+in+Activated+Sludge.">Relationship of Species-Specific Filament Levels to Filamentous Bulking in Activated Sludge.</a> Applied and Environmental Microbiology. 70 (4), 2420-2428 (2004).</li><li>Cromey, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Avoiding+twisted+pixels:+ethical+guidelines+for+the+appropriate+use+and+manipulation+of+scientific+digital+images.">Avoiding twisted pixels: ethical guidelines for the appropriate use and manipulation of scientific digital images.</a> Science and Engineering Ethics. 16 (4), 639-667 (2010).</li><li>Wickham, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tidy+Data.">Tidy Data.</a> Journal of Statistical Software. 59 (10), (2014).</li><li>van Rossum, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Python tutorial. , (1995).</li><li>Schindelin, J., Arganda-Carreras, I., Frise, E. <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> Nature Methods. 9 (7), 676-682 (2012).</li><li>. SParMorIA: Sludge Particle Morphological ImageAnalysis Available from: <a target="_blank" href="https://github.com/joeweaver/SParMorIA-Sludge-Particle-Morphological-Image-Analysis">https://github.com/joeweaver/SParMorIA-Sludge-Particle-Morphological-Image-Analysis</a> (2018)</li><li>Ferreira, T., Rasband, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> ImageJ User Guide: IJ 1.42 r. , (2012).</li><li>Sezgin, M., Sankur, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Survey+over+image+thresholding+techniques+and+quantitative+performance+evaluation.">Survey over image thresholding techniques and quantitative performance evaluation.</a> Journal of Electronic Imaging. 13 (1), 146-166 (2004).</li><li>Kr&#246;ner, S., Dom&#233;nech Carb&#243;, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+minimum+pixel+resolution+for+shape+analysis:+Proposal+of+a+new+data+validation+method+for+computerized+images.">Determination of minimum pixel resolution for shape analysis: Proposal of a new data validation method for computerized images.</a> Powder Technology. 245, 297-313 (2013).</li><li>McKinney, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Data+Structures+for+Statistical+Computing+in+Python.">Data Structures for Statistical Computing in Python.</a> Proceedings of the 9th Python in Science Conference. , 51-56 (2010).</li><li>Waskom, 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=.">.</a> seaborn: v0.5.0 (November 2014). , (2014).</li><li>. dplyr: A Grammar of Data Manipulation Available from: <a target="_blank" href="https://cran.r-project.org/web/packages/dplyr/index.html">https://cran.r-project.org/web/packages/dplyr/index.html</a> (2016)</li><li>Riley, R. S., Ben-Ezra, J. M., Massey, D., Slyter, R. L., Romagnoli, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Digital+Photography:+A+Primer+for+Pathologists.">Digital Photography: A Primer for Pathologists.</a> Journal of Clinical Laboratory Analysis. 18 (2), 91-128 (2004).</li><li>Singh, S., Bray, M. A., Jones, T. R., Carpenter, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pipeline+for+illumination+correction+of+images+for+high-throughput+microscopy.">Pipeline for illumination correction of images for high-throughput microscopy.</a> Journal of Microscopy. 256 (3), 231-236 (2014).</li><li>Eastwood, B. S., Childs, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Image+Alignment+for+Multiple+Camera+High+Dynamic+Range+Microscopy.">Image Alignment for Multiple Camera High Dynamic Range Microscopy.</a> Proceedings. IEEE Workshop on Applications of Computer Vision. , 225-232 (2012).</li><li>High Dynamic Range Microscopy for Cytopathological Cancer Diagnosis. IEEE Journal of Selected Topics in Signal Processing (Special Issue on: Digital Image Processing Techniques for Oncology) Available from: <a target="_blank" href="https://www.lfb.rwth-aachen.de/en/">https://www.lfb.rwth-aachen.de/en/</a> (2009)</li><li>Jain, 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=Supervised+Learning+of+Image+Restoration+with+Convolutional+Networks.">Supervised Learning of Image Restoration with Convolutional Networks.</a> 2007 IEEE 11th International Conference on Computer Vision. , 1-8 (2007).</li></ol>

虽然图像分析系统相当强大, 并采取了 qc 步骤, 以确保不良图像被删除, 但适当注意采样、制版和图像采集中的具体问题可以提高数据的准确性和图像的比例。图像通过 qc。
采样浓度 假设已采取具有代表性的样品, 最重要的步骤是确保有足够的粒子存在于具有代表性的 9和高效的分析中, 同时不会使粒子重叠。
这相当于在?...

该方法的目的是提供一种明确定义的、可重复的和部分自动化的方法, 用于确定生物反应器中颗粒的大小和形状分布, 特别是那些含有活性污泥絮凝剂和好氧颗粒的生物反应器中颗粒的大小和形状分布1,2. 这种方法背后的理由是提高我们现有的内部协议3、4 的可负担性、简单性、吞吐量和可重复性, 方便为他人测量颗粒, 并促进共享和数据的比较。
粒子测量分析有两大类--直接成像和使用光散射5等特性的推理方法。虽然推理方法可以自动化, 并且具有较大的吞吐量, 但设备成本很高。此外, 虽然推理方法可以准确地确定粒子6的等效大小, 但它们没有提供详细的形状信息7。
由于需要形状数据, 我们的方法基于直接成像。虽然存在一些高通量的成像方法, 但它们传统上需要昂贵的商业硬件或自定义构建的解决方案8,9。我们的方法是为了使用通用的、经济实惠的硬件和软件, 这些硬件和软件虽然吞吐量减少, 但产生的粒子图像远远超过许多分析10所需的最小值.
现有协议可能没有指定重要的采样和图像采集步骤。其他协议可以指定引入主观偏差的手动步骤 (如临时阈值11)。一个明确定义的方法, 指定采样, 固定和图像采集步骤结合免费提供的分析软件将加强实验室内的图像分析和实验室之间的比较。该协议的一个主要目标是提供一个工作流和工具, 该工作流和工具应能为同一样本带来来自不同实验室的可重现结果。
除了对图像分析过程进行规范化外, 此管道生成的数据还记录在一个定义明确、格式良好的文件12中, 适合流行的数据分析包13、14、缓动实验使用特定分析 (如自定义图形生成), 并促进实验室之间的数据共享。
该协议特别适用于需要颗粒形状数据、无法获得推理方法、不希望开发自己的图像分析管道、希望与他人轻松共享数据的研究人员

<table>
	<tbody>
		<tr>
			<td>10% Bleach solution</td>
			<td>Chlorox</td>
			<td>31009</td>
			<td>For workspace disinfection.</td>
		</tr>
		<tr>
			<td>15 mL centrifuge tube with cap</td>
			<td>Corning</td>
			<td>430790</td>
			<td>Per sample.</td>
		</tr>
		<tr>
			<td>50 mL Erlenmeyer flask</td>
			<td>Corning</td>
			<td>4980-50</td>
			<td>Other vessels are suitable so long as they can contain &#62; 40 mL of sample and allow mixing</td>
		</tr>
		<tr>
			<td>500 mL Kimax Bottle</td>
			<td>Kimble-Chase</td>
			<td>14395-50</td>
			<td>Or otherwise sufficient for agar handling</td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>BD</td>
			<td>214010</td>
			<td>Solid, to prepare 7.5% gel. 7 mL per sample.</td>
		</tr>
		<tr>
			<td>Data analysis software</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>R or Python are suggested</td>
		</tr>
		<tr>
			<td>Deionized water</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Sufficient to prepare stain and agar. If unavailable, tap should be fine.</td>
		</tr>
		<tr>
			<td>Desktop computer</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Image analysis is not CPU intensive, any &#39;ordinary&#39; desktop computer circa 2017 should be sufficient.</td>
		</tr>
		<tr>
			<td>External hard drive</td>
			<td>Seagate</td>
			<td>STEB5000100</td>
			<td>Not fully required, but extremely useful given the number an size of images. 2 or more TB of storage suggested.</td>
		</tr>
		<tr>
			<td>FIJI</td>
			<td>NIH</td>
			<td>version 1.51d</td>
			<td>Version is ImageJ core. Plugins are updated as of writing. Available at: https://imagej.net/Fiji/Downloads</td>
		</tr>
		<tr>
			<td>GIT</td>
			<td>Open Source</td>
			<td>version 2.19.1 or later</td>
			<td>Available at: https://git-scm.com/</td>
		</tr>
		<tr>
			<td>Image capture software</td>
			<td>ToupView</td>
			<td>version 3.7.5177</td>
			<td>Any compatible with camera, may come with camera. Should allow saving TIFF images with spatial calibration data.</td>
		</tr>
		<tr>
			<td>Mechanical (X/Y) Stage</td>
			<td>OMAX</td>
			<td>A512</td>
			<td>Not fully required, but greatly aids image acquisition.</td>
		</tr>
		<tr>
			<td>Methylene blue</td>
			<td>Fisher</td>
			<td>M291-100</td>
			<td>Solid, to prepare 1% w/v solution. 5 uL solution per sample.</td>
		</tr>
		<tr>
			<td>Microscope camera</td>
			<td>OMAX</td>
			<td>A35140U</td>
			<td>Any digitial camera compatible with microscope. Resolution providing at least 5 um per pixel at 10x magnification and a dynamic range of at least 8 bits per pixel per color channel is suggested.</td>
		</tr>
		<tr>
			<td>Optical Stage Micrometer</td>
			<td>OMAX</td>
			<td>A36CALM1</td>
			<td>Or otherwise sufficient for spatial calibration.</td>
		</tr>
		<tr>
			<td>Petri dish, 100 mm</td>
			<td>Fisher</td>
			<td>FB0875712</td>
			<td>1 per sample.</td>
		</tr>
		<tr>
			<td>PPE</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Standard lab coat, gloves, and eyewear.</td>
		</tr>
		<tr>
			<td>Sparmoria macro</td>
			<td>NCSU</td>
			<td>version 0.2.1</td>
			<td>Available at github repository : https://github.com/joeweaver/SParMorIA-Sludge-Particle-Morphological-Image-Analysis</td>
		</tr>
		<tr>
			<td>Stereo/dissecting microscope</td>
			<td>Nikon</td>
			<td>SMZ-2T</td>
			<td>Should provide 10 to 20x magnficiation and allow digital photos either with a buit-in camera or profide a mounting point for a CCD.</td>
		</tr>
	</tbody>
</table>

measuring the shape and size of activated sludge particles immobilized in agar with an open source software pipeline

实验生物反应器, 如处理废水的生物反应器, 含有其大小和形状是重要参数的颗粒。例如, 活性污泥絮凝剂的大小和形状可以指示微尺度上的条件, 也直接影响污泥在澄清器中的沉降情况。
粒子大小和形状都是错误的 "简单" 测量。在采样、成像和分析粒子时, 可能会出现许多微妙的问题, 这些问题通常在非正式协议中没有得到解决。采样方法可能有偏差或没有提供足够的统计能力。样品本身可能保存不良或在固定过程中发生改变。图像的质量可能不够;重叠粒子、景深、放大倍率和各种噪声都会产生较差的结果。不明确的分析可能会引入偏差, 例如通过手动图像阈值和分割产生的偏差。
除了可重复性之外, 可负担性和吞吐量也是可取的。一种经济实惠、高吞吐量的方法可以实现更频繁的颗粒测量, 从而产生许多包含数千个粒子的图像。一种使用廉价试剂、通用解剖显微镜和自由可用的开源分析软件的方法允许可重复、可访问、可重复和部分自动化的实验结果。此外, 这种方法的产品可以格式良好, 定义明确, 易于理解的数据分析软件, 方便实验室内分析和实验室之间的数据共享。
我们提出了一个协议, 详细介绍了生产此类产品所需的步骤, 包括: 采样、样品制备和琼脂固定、数字图像采集、数字图像分析, 以及来自分析结果。我们还包括了一个开源数据分析管道来支持这一协议。

生成的文件 图 1所示的过程将在分析的每个图像中生成两个文件。第一个文件是一个逗号分隔值 (csv) 文本文件, 其中每一行对应于单个粒子, 列描述各种粒子度量, 如面积、循环和固体, 并在 imagej 手册17中定义。示例 csv 文件作为补充信息和示例数据目录中包含。
<img alt="Fi...

Watch this Scientific Journal Video about Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline at JoVE.com

Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline

活性污泥中颗粒的大小和形状是用不同方法测量的重要参数。不具有代表性的采样、次优图像和主观分析参数产生了不准确之处。为了最大限度地减少这些错误并便于测量, 我们提供了一个协议, 指定每个步骤, 包括开源软件管道。

利用开源软件管道测量琼脂中固定活性污泥颗粒的形状和大小

Experimental bioreactors, such as those treating wastewater, contain particles whose size and shape are important parameters. For example, the size and ...

活性污泥颗粒的大小和形状对废水处理效率至关重要。然而，他们的测量往往是临时性的。该协议为测量提供了可重复、定义良好和半自动化的测量方法。该协议的主要优点是，它可以测量大量颗粒在广泛的形态，同时减少主观和系统偏差。虽然这项技术侧重于活性污泥，但从技术上讲，任何具有相同颗粒形态的东西，如微塑料，都可以用这种方法进行测量。首次尝试此技术时，尝试一次制作一个板，并练习制作该板的物理运动。此外，花你的时间与显微镜。本文的视频版本很重要，因为采样和板准备需要很多最好在视觉上传达的小技术。此外，展示和看到良好的板图片对于确保可重复性非常重要。今天演示这个协议的是约瑟夫 ·韦弗，我实验室的博士生。首先，从反应堆的混合部分获取一个具有代表性的样品。轻轻混合样品，然后立即将确定的样品体积倒入 15 毫升离心管中。接下来在每个样品中加入五升百分之一的甲基蓝微升。轻轻反转管子至少三次，将样品盖住并混合。在室温下，允许样品染色至少5分钟，但不超过30分钟。一旦染色，将足够体积的熔化7.5%的加糖和去化水转移到离心管，使总管体积达到6.5至9毫升之间。然后重述离心管，轻轻反转至少三次，将样品混合到搅拌器中。一边把帽子指向远离自己，一边打开帽子。将每个管子的管内物倒入自己的100毫升塑料培养皿中，同时轻轻摇动盘子，实现完全、光滑的涂层和颗粒的视觉均匀分布。让板在室温下冷却至少 5 分钟，直到加糖凝固。将未覆盖的板面朝上放在可放大 10 到 20 倍的立体显微镜的显微镜舞台上。使用 LED 照明支架或灯板等设备，均匀地使用漫反射灯从下方照亮样品。打开图像捕获软件，确保显微镜光线路径设置为照片。然后，从相机列表中选择相应的摄像机。调整显微镜，使多个粒子出现在具有大、定义良好的边缘的焦点平面中。使用 10 到 20 倍的放大倍率测量粒子，同时保持相对较深的焦点平面。暂时取下阿加糖板，将千分尺放在舞台上。调整精细对焦，直到微米上的脱离在图像捕获软件中出现尖锐聚焦。并校准像素与微米的比率。接下来，通过单击视图并选择实际大小，将缩放设置为 100%。然后选择选项并转到校准。在这里，沿微米长轴将主视口中的红色校准条对齐。垂直条以零和 200 微米分月为中心。在校准对话框中，输入当前放大级别和 200 微米的实际长度。如果已校准，请从菜单栏中选择放大倍率，然后选择当前放大级别以确认校准。在测量菜单中，转到行并选择任意行。单击千分米的零分子和长轴的交点。然后再次单击 200 微米线和长轴处的交点。正确的校准应显示为大约 200 微米。通过单击选择对象按钮、单击线条、按删除键和按确认框上的"是"来删除行。接下来，更换加糖板并调整精细对焦，以实现成像软件中的最大细节。为此，首先通过选择摄像机侧边栏的位深度面板中的单选按钮来增加允许的最大值的位深度。此外，通过选择相机侧边栏的颜色等级面板中适当的单选按钮，将软件设置为获取灰度图像。现在，在曝光和直方图之间折叠任何打开的侧边栏面板。将增益减小为 1 并增加曝光，直到视口中出现清晰的图像，直到直方图显示为直方图框的任一端未剪切的分布。调整直方图以避免过度和暴露。在摄像机侧边栏的直方图面板中，将直方图的左边界滑到最低值之外，将右边界滑到最高值之外。将图像另存为未压缩的 TIF 文件。通过保存时使用校准信息框检查保存，在图像元数据中包含放大信息。选择另一个与上一张图像不重叠的区域，该路径在板下移动时从左到右和从右到左交替。捕获至少 500 个视觉估计粒子进行分析。通过克隆 GIT 存储库获取粒子分析代码。在命令行中，通过键入此处显示的命令来检索代码的最新版本。按照克隆存储库的顶层目录中的 read me 文本文件中的说明安装分析代码。接下来，编辑一个文本文件，列出要处理的目录以及可选参数。有关参数和示例的列表，请参阅示例和分析子目录。现在，通过键入此处显示的命令，在命令行上运行分析。斐济路径是 imageJ-win64 的目录。exe 位于。并参数描述分析设置的文本文件的位置。可执行文件的名称可能因安装 Fiji 操作系统而异。分析将自动运行，并且需要几分钟到几个小时，具体取决于图像的大小和数量。接下来，检查位于指定输出目录的叠加子目录中的质量控制文件。注意具有杂散雾或捕获不良粒子的图像，所有图像都显示为与背景不匹配的阴影轮廓。就是这样。数据现已准备好用于实验特定分析和图形生成。虽然没有粒子阈值方法是完美的，但下面是可接受的结果示例。在评估 QC 映像时，发现三个常见错误。未能准确符合粒子边界、无法识别粒子和工件包含。在这里，显示两个实验反应堆之间的粒子分布，并结合研究人员指出的定性元数据。此图表显示，在这种情况下，反应器的粒径分布通常相似，随着时间的推移，这些分布趋于较大均值和较宽的分布。执行此过程时，必须均匀地涂上一层薄薄的加糖，其中含有均匀分布的颗粒。一定要练习，花些时间。除了这个程序，有趣的粒子可以从阿加中切除并研究。在数据方面，从该协议生成的文件被很好地定义，天空是分析的限制。这项技术为提供对有氧颗粒污泥的新见解铺平了道路。它形态是非常重要的，它允许我们以标准的方式测量它。废水在生物学上是活跃的。生物安全一级做法受到鼓励。此外，在微波时，agar 如何冒泡，并在打开离心管时喷洒热液滴。

Research

JoVE Journal

Environment

Measuring Fluxes of Mineral Nutrients and Toxicants in Plants with Radioactive Tracers

植物与放射性示踪剂测量矿质营养和毒物的通量

Unidirectional influx and efflux of nutrients and toxicants, and their resultant net fluxes, are central to the nutrition and toxicology of plants. ...

科研

环境科学

Development of Sulfidogenic Sludge from Marine Sediments and Trichloroethylene Reduction in an Upflow Anaerobic Sludge Blanket Reactor

Sulfidogenic污泥海洋沉积物和三氯乙烯减少在上流式厌氧污泥床反应器开发

The importance of microbial sulfate reduction relies on the various applications that it offers in environmental biotechnology. Engineered sulfate ...

Measuring Rates of Herbicide Metabolism in Dicot Weeds with an Excised Leaf Assay

测量除草剂代谢的双子叶杂草价格与切下的叶片分析

In order to isolate and accurately determine rates of herbicide metabolism in an obligate-outcrossing dicot weed, waterhemp (Amaranthus tuberculatus), we ...

Spotting Cheetahs: Identifying Individuals by Their Footprints

通过他们的足迹识别个体：合模猎豹

The cheetah (Acinonyx jubatus) is Africa's most endangered large felid and listed as Vulnerable with a declining population trend by the IUCN1. It ranges ...

Extraction of Structural Extracellular Polymeric Substances from Aerobic Granular Sludge

从好氧颗粒污泥结构胞外聚合物的提取

To evaluate and develop methodologies for the extraction of gel-forming extracellular polymeric substances (EPS), EPS from aerobic granular sludge (AGS) ...

An Ultra-clean Multilayer Apparatus for Collecting Size Fractionated Marine Plankton and Suspended Particles

海洋浮游生物和悬浮颗粒的超洁净多层采集装置

The distributions of many trace elements in the ocean are strongly associated with the growth, death, and re-mineralization of marine plankton and those ...

Experimental Study of the Relationship Between Particle Size and Methane Sorption Capacity in Shale

页岩中粒径与甲烷吸附能力关系的实验研究

The amount of adsorbed shale gas is a key parameter used in shale gas resource evaluation and target area selection, and it is also an important standard ...

Measuring Hypopharyngeal Gland Acinus Size in Honey Bee (Apis mellifera) Workers

Measuring Hypopharyngeal Gland Acinus Size in Honey Bee Apis mellifera Workers

蜂蜜蜂 (api 蜜蜂) 中下咽腺性腺泡大小的测定

The nurse hypopharyngeal glands produce the protein fraction of the worker and royal jelly that is fed to developing larvae and queens. These paired ...

Combining Eye-tracking Data with an Analysis of Video Content from Free-viewing a Video of a Walk in an Urban Park Environment

将眼动追踪数据与从自由观看城市公园环境中的步行视频中获得的视频内容进行分析

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. ...

BtM, a Low-cost Open-source Datalogger to Estimate the Water Content of Nonvascular Cryptogams

BtM, 一种低成本的开源数据采集器, 用于估算非血管化机制的含水量

Communities of nonvascular cryptogams, such as mosses or lichens, are an important part of the Earth's biodiversity, contributing to the regulation of the ...