CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data.
CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data.
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DOI：
10.1186/s12868-022-00751-7
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发表时间：
2022-11-30
期刊：
影响因子：
2.4
通讯作者：
Page, Stephanie Cerceo
中科院分区：
文献类型：
--
作者：
Tippani, Madhavi;Pattie, Elizabeth A.;Davis, Brittany A.;Nguyen, Claudia V.;Wang, Yanhong;Sripathy, Srinidhi Rao;Maher, Brady J.;Martinowich, Keri;Jaffe, Andrew E.;Page, Stephanie Cerceo
钙成像是一种记录大量神经元细胞活动的强大技术。然而，缺乏能够在培养的神经元中进行单细胞分辨率的分析方法，特别是对于源自人类诱导多能干细胞（hiPSC）的培养物。现有方法缺乏可扩展性，无法适应多条线之间、跨发育时间点或跨药理操作的高通量比较。为了满足这一需求，我们开发了 CaPTure，一种可扩展的自动化 Ca2+ 成像分析管道 (https://github.com/LieberInstitute/CaPTure)。 CaPTure 检测神经元，对自发活动进行分类和量化，量化同步指标，并生成有助于表型发现的细胞和网络特定指标。该方法与计算集群上的并行处理兼容，不需要大量的用户输入或参数修改。 CaPTure 允许以细胞分辨率快速评估培养细胞中的神经元活动，使其适合高通量筛选和表型发现。该平台可应用于人类和啮齿动物源性神经元，并且与许多成像系统兼容。在线版本包含可在 10.1186/s12868-022-00751-7 获取的补充材料。
Calcium imaging is a powerful technique for recording cellular activity across large populations of neurons. However, analysis methods capable of single-cell resolution in cultured neurons, especially for cultures derived from human induced pluripotent stem cells (hiPSCs), are lacking. Existing methods lack scalability to accommodate high-throughput comparisons between multiple lines, across developmental timepoints, or across pharmacological manipulations. To address this need we developed CaPTure, a scalable, automated Ca2+ imaging analysis pipeline (https://github.com/LieberInstitute/CaPTure). CaPTuredetects neurons, classifies and quantifies spontaneous activity, quantifies synchrony metrics, and generates cell- and network-specific metrics that facilitate phenotypic discovery. The method is compatible with parallel processing on computing clusters without requiring significant user input or parameter modification. CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems. The online version contains supplementary material available at 10.1186/s12868-022-00751-7.
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DOI：
10.1083/jcb.201004104
发表时间：
2010-05-31
期刊：
The Journal of cell biology
影响因子：
--
作者：
Linkert M;Rueden CT;Allan C;Burel JM;Moore W;Patterson A;Loranger B;Moore J;Neves C;Macdonald D;Tarkowska A;Sticco C;Hill E;Rossner M;Eliceiri KW;Swedlow JR
通讯作者：
Swedlow JR
影响因子：
3
作者：
Patel TP;Man K;Firestein BL;Meaney DF
通讯作者：
Meaney DF
影响因子：
16.2
作者：
Mukamel, Eran A.;Nimmerjahn, Axel;Schnitzer, Mark J.
通讯作者：
Schnitzer, Mark J.
影响因子：
2.4
作者：
Artimovich E;Jackson RK;Kilander MBC;Lin YC;Nestor MW
通讯作者：
Nestor MW
影响因子：
3.5
作者：
Cantu, Daniel A.;Wang, Bo;Portera-Cailliau, Carlos
通讯作者：
Portera-Cailliau, Carlos