• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

波形图分析软件Clear和波形图分析软件Direct：用于使用波形图对分子和细胞动力学进行自动定量分析的两种工具。

KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs.

作者信息

Mangeol Pierre, Prevo Bram, Peterman Erwin J G

机构信息

Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam NH 1081HV, Netherlands.

Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam NH 1081HV, Netherlands

出版信息

Mol Biol Cell. 2016 Jun 15;27(12):1948-57. doi: 10.1091/mbc.E15-06-0404. Epub 2016 Apr 20.

DOI:10.1091/mbc.E15-06-0404
PMID:27099372
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4907728/
Abstract

Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way.

摘要

动态过程在活细胞中无处不在且至关重要。为了恰当地理解这些过程，必须以时间依赖的方式对其进行测量，并对所得数据进行定量分析，最好使用自动化工具。波形图是表示动态过程运动的单张图像，广泛应用于活细胞成像。尽管它们包含了完整的动态范围，但要以可靠的方式提取这些定量信息并非易事。在此，我们展示了两个互补的、公开可用的软件工具，即KymographClear和KymographDirect，它们能够揭示动态过程的详细信息。KymographClear是用于ImageJ的宏工具集，用于生成波形图，可对不同运动方向进行自动颜色编码。KymographDirect是一个独立工具，能够以自动化方式从广泛的动态过程中获取的波形图中提取定量信息，具有高精度和可靠性。我们讨论了这些软件工具背后的概念，使用模拟数据对其进行验证，并在实验数据上对其进行测试。我们表明，这些工具可用于以自动化且用户友好的方式从各种细胞生物学实验中提取运动参数。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/1cc0bb1fd13b/1948fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/984904f6facc/1948fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/bd8264ffc63c/1948fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/472526bec656/1948fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/a617fd4cdd5b/1948fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/d258b72a36a2/1948fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/b119cb4a8a27/1948fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/edc07206ae6d/1948fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/e4ac2779f0a6/1948fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/6d31142070ee/1948fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/1cc0bb1fd13b/1948fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/984904f6facc/1948fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/bd8264ffc63c/1948fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/472526bec656/1948fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/a617fd4cdd5b/1948fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/d258b72a36a2/1948fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/b119cb4a8a27/1948fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/edc07206ae6d/1948fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/e4ac2779f0a6/1948fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/6d31142070ee/1948fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b48/4907728/1cc0bb1fd13b/1948fig10.jpg

相似文献

1
KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs.波形图分析软件Clear和波形图分析软件Direct：用于使用波形图对分子和细胞动力学进行自动定量分析的两种工具。
Mol Biol Cell. 2016 Jun 15;27(12):1948-57. doi: 10.1091/mbc.E15-06-0404. Epub 2016 Apr 20.
2
KymoButler, a deep learning software for automated kymograph analysis.KymoButler，一款用于自动示波图分析的深度学习软件。
Elife. 2019 Aug 13;8:e42288. doi: 10.7554/eLife.42288.
3
Automated Multi-Peak Tracking Kymography (AMTraK): A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy.自动多峰跟踪记波法（AMTraK）：一种以亚像素精度量化亚细胞动力学的工具。
PLoS One. 2016 Dec 19;11(12):e0167620. doi: 10.1371/journal.pone.0167620. eCollection 2016.
4
MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules.MTrack：动态微管的自动检测、跟踪和分析。
Sci Rep. 2019 Mar 7;9(1):3794. doi: 10.1038/s41598-018-37767-1.
5
Automated registration of multispectral MR vessel wall images of the carotid artery.颈动脉多光谱磁共振血管壁图像的自动配准。
Med Phys. 2013 Dec;40(12):121904. doi: 10.1118/1.4829503.
6
User-friendly tools for quantifying the dynamics of cellular morphology and intracellular protein clusters.用于量化细胞形态动力学和细胞内蛋白质簇的用户友好型工具。
Methods Cell Biol. 2014;123:409-27. doi: 10.1016/B978-0-12-420138-5.00022-7.
7
Microtubule dynamics analysis using kymographs and variable-rate particle filters.使用时间轨迹图和变速粒子滤波器分析微管动力学。
IEEE Trans Image Process. 2010 Jul;19(7):1861-76. doi: 10.1109/TIP.2010.2045031. Epub 2010 Mar 11.
8
SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells.SuperSegger：细菌细胞的稳健图像分割、分析及谱系追踪
Mol Microbiol. 2016 Nov;102(4):690-700. doi: 10.1111/mmi.13486. Epub 2016 Sep 23.
9
Open source software for quantification of cell migration, protrusions, and fluorescence intensities.用于细胞迁移、突起和荧光强度定量分析的开源软件。
J Cell Biol. 2015 Apr 13;209(1):163-80. doi: 10.1083/jcb.201501081. Epub 2015 Apr 6.
10
PatternJ: an ImageJ toolset for the automated and quantitative analysis of regular spatial patterns found in sarcomeres, axons, somites, and more.PatternJ：一个 ImageJ 工具集，用于自动和定量分析在肌节、轴突、体节等中发现的规则空间模式。
Biol Open. 2024 Jun 15;13(6). doi: 10.1242/bio.060548. Epub 2024 Jun 18.

引用本文的文献

1
DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins.DNA聚合酶能主动且有序地取代单链DNA结合蛋白。
Nat Commun. 2025 Aug 12;16(1):7431. doi: 10.1038/s41467-025-62531-1.
2
Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout.基因编码的模块化亚细胞器探针揭示了由PRKN基因敲除驱动的溶酶体和线粒体功能障碍。
iScience. 2025 Jun 3;28(7):112816. doi: 10.1016/j.isci.2025.112816. eCollection 2025 Jul 18.
3
Cellular anatomy of arbuscular mycorrhizal fungi.

本文引用的文献

1
Functional differentiation of cooperating kinesin-2 motors orchestrates cargo import and transport in C. elegans cilia.合作型肌球蛋白-2 分子马达的功能分化协调秀丽隐杆线虫纤毛中的货物导入和运输。
Nat Cell Biol. 2015 Dec;17(12):1536-45. doi: 10.1038/ncb3263. Epub 2015 Nov 2.
2
Advanced methods of microscope control using μManager software.使用μManager软件的高级显微镜控制方法。
J Biol Methods. 2014;1(2). doi: 10.14440/jbm.2014.36.
3
Simple and direct assembly of kymographs from movies using KYMOMAKER.使用 KYMOMAKER 从电影中简单直接地组装动画。
丛枝菌根真菌的细胞解剖学
Curr Biol. 2025 Jun 9;35(11):R545-R562. doi: 10.1016/j.cub.2025.03.053.
4
DYF-5 regulates intraflagellar transport by affecting train turnaround.DYF-5通过影响列车折返来调节鞭毛内运输。
Mol Biol Cell. 2025 May 1;36(5):ar53. doi: 10.1091/mbc.E24-08-0378. Epub 2025 Mar 12.
5
Chronic Oxidative Stress and Stress Granule Formation in UBQLN2 ALS Neurons: Insights into Neuronal Degeneration and Potential Therapeutic Targets.泛素样蛋白2（UBQLN2）相关肌萎缩侧索硬化症（ALS）神经元中的慢性氧化应激与应激颗粒形成：对神经元变性及潜在治疗靶点的见解
Int J Mol Sci. 2024 Dec 15;25(24):13448. doi: 10.3390/ijms252413448.
6
MYO18B promotes lysosomal exocytosis by facilitating focal adhesion maturation.肌球蛋白18B（MYO18B）通过促进粘着斑成熟来促进溶酶体胞吐作用。
J Cell Biol. 2025 Mar 3;224(3). doi: 10.1083/jcb.202407068. Epub 2025 Jan 3.
7
Ciliary length regulation by intraflagellar transport in zebrafish.斑马鱼中鞭毛内运输对纤毛长度的调节
Elife. 2024 Dec 13;13:RP93168. doi: 10.7554/eLife.93168.
8
The kinetochore protein KNL-1 regulates the actin cytoskeleton to control dendrite branching.动粒蛋白KNL-1调节肌动蛋白细胞骨架以控制树突分支。
J Cell Biol. 2025 Feb 3;224(2). doi: 10.1083/jcb.202311147. Epub 2024 Dec 3.
9
Thymine DNA glycosylase combines sliding, hopping, and nucleosome interactions to efficiently search for 5-formylcytosine.胸腺嘧啶 DNA 糖基化酶通过滑动、跳跃和核小体相互作用，有效地搜索 5-羟甲基胞嘧啶。
Nat Commun. 2024 Oct 25;15(1):9226. doi: 10.1038/s41467-024-53497-7.
10
How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors.如何使用混杂识别而无需钳夹来扫描裸露的 DNA：先锋转录因子的模型。
Nucleic Acids Res. 2024 Oct 14;52(18):11098-11114. doi: 10.1093/nar/gkae790.
Traffic. 2014 Jan;15(1):1-11. doi: 10.1111/tra.12127. Epub 2013 Oct 31.
4
PICH: a DNA translocase specially adapted for processing anaphase bridge DNA.PICH：一种专门用于处理后期桥 DNA 的 DNA 转位酶。
Mol Cell. 2013 Sep 12;51(5):691-701. doi: 10.1016/j.molcel.2013.07.016. Epub 2013 Aug 22.
5
STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA.受激发射损耗纳米显微镜结合光镊揭示了在密集覆盖的 DNA 上的蛋白质动力学。
Nat Methods. 2013 Sep;10(9):910-6. doi: 10.1038/nmeth.2599. Epub 2013 Aug 11.
6
Microtubule-sliding activity of a kinesin-8 promotes spindle assembly and spindle-length control.驱动蛋白-8 的微管滑动活性促进纺锤体的组装和纺锤体长度的控制。
Nat Cell Biol. 2013 Aug;15(8):948-57. doi: 10.1038/ncb2801. Epub 2013 Jul 14.
7
Intraflagellar transport drives flagellar surface motility.鞭毛内运输驱动鞭毛表面运动。
Elife. 2013 Jun 11;2:e00744. doi: 10.7554/eLife.00744.
8
Synergy between XMAP215 and EB1 increases microtubule growth rates to physiological levels.XMAP215 和 EB1 的协同作用将微管生长速度提高到生理水平。
Nat Cell Biol. 2013 Jun;15(6):688-93. doi: 10.1038/ncb2744. Epub 2013 May 12.
9
NIH Image to ImageJ: 25 years of image analysis.NIH 图像到 ImageJ：25 年的图像分析。
Nat Methods. 2012 Jul;9(7):671-5. doi: 10.1038/nmeth.2089.
10
The BBSome controls IFT assembly and turnaround in cilia.BBSome 控制纤毛内的IFT 组装和周转。
Nat Cell Biol. 2012 Sep;14(9):950-7. doi: 10.1038/ncb2560. Epub 2012 Aug 26.