Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.
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DOI：
10.1371/journal.pcbi.1006157
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发表时间：
2018-05
影响因子：
4.3
通讯作者：
Bethge M
中科院分区：
文献类型：
--
作者：
Berens P;Freeman J;Deneux T;Chenkov N;McColgan T;Speiser A;Macke JH;Turaga SC;Mineault P;Rupprecht P;Gerhard S;Friedrich RW;Friedrich J;Paninski L;Pachitariu M;Harris KD;Bolte B;Machado TA;Ringach D;Stone J;Rogerson LE;Sofroniew NJ;Reimer J;Froudarakis E;Euler T;Román Rosón M;Theis L;Tolias AS;Bethge M
近年来，双光子钙成像已成为一个标准的工具，以探测神经回路的功能和研究在神经元群体的计算。然而，由于荧光钙指示剂的动力学相对较慢，所获得的信号仅是神经活动的间接测量。过去已经提出了不同的算法来从有噪声的钙测量中估计尖峰速率，但是性能可以提高到什么程度是一个悬而未决的问题。在这里，我们报告了spikefinder挑战赛的结果，该挑战赛旨在通过众包促进新的尖峰速率推理算法的发展。我们提出了10个提交的算法，表现出改进的性能相比，以前评估的方法。有趣的是，表现最好的算法基于从深度神经网络到生成模型的广泛原则，但提供了高度相关的神经活动估计。竞赛表明，基准挑战可以推动神经科学中的算法发展。双光子钙成像是研究大脑中大量神经元活动的主要工具之一。在这种技术中，当神经元由于细胞内钙的相关增加而激发动作电位时，荧光钙指示剂改变其亮度。然而，尽管已经提出了许多算法来从测量的信号估计尖峰速率，但问题远未解决。我们组织了一个公开的比赛，使用的数据集，地面实况数据可用。参与者获得了一个训练集来开发新的算法，并在隐藏的测试集上评估了算法的性能。在这里，我们报告的结果，这场比赛，并讨论了更好的算法来推断尖峰活动的成像数据取得的进展。
In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience. Two-photon calcium imaging is one of the major tools to study the activity of large populations of neurons in the brain. In this technique, a fluorescent calcium indicator changes its brightness when a neuron fires an action potential due to an associated increase in intracellular calcium. However, while a number of algorithms have been proposed for estimating spike rates from the measured signal, the problem is far from solved. We organized a public competition using a data set for which ground truth data was available. Participants were given a training set to develop new algorithms, and the performance of the algorithms was evaluated on a hidden test set. Here we report on the results of this competition and discuss the progress made towards better algorithms to infer spiking activity from imaging data.
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影响因子：
3.4
作者：
Wilt, Brian A.;Fitzgerald, James E.;Schnitzer, Mark J.
通讯作者：
Schnitzer, Mark J.
影响因子：
19.5
作者：
Russakovsky, Olga;Deng, Jia;Fei-Fei, Li
通讯作者：
Fei-Fei, Li
影响因子：
2.5
作者：
Vogelstein, Joshua T.;Packer, Adam M.;Paninski, Liam
通讯作者：
Paninski, Liam
影响因子：
16.2
作者：
Theis L;Berens P;Froudarakis E;Reimer J;Román Rosón M;Baden T;Euler T;Tolias AS;Bethge M
通讯作者：
Bethge M
影响因子：
16.2
作者：
Pnevmatikakis EA;Soudry D;Gao Y;Machado TA;Merel J;Pfau D;Reardon T;Mu Y;Lacefield C;Yang W;Ahrens M;Bruno R;Jessell TM;Peterka DS;Yuste R;Paninski L
通讯作者：
Paninski L