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About cai-3

Description of dataset cai-3 (calcium imaging 3).

Summary of the data

This dataset provides data from N=50 neurons measured simultaneously using two-photon calcium imaging and electrophysiology in the mouse retina and visual cortex using different recording techniques, scanning rates and indicators. Importantly, all data has been acquired under typical population recording conditions in anesthetized and awake animals.

This dataset has been assembled for benchmarking spike inference algorithms:

Theis, L., Berens, P., Froudarakis, E., Reimer, J., Rosón, M. R., Baden, T., Euler T., Tolias, A.S. & Bethge, M. (2016). Benchmarking spike rate inference in population calcium imaging. Neuron, 90(3), 471-482. doi:

In addition, parts of the data were used in the following publications:

Baden, T., Berens, P., Franke, K., Rosón, M. R., Bethge, M., & Euler, T. (2016). The functional diversity of retinal ganglion cells in the mouse. Nature, 529(7586), 345-350. doi:10.1038/nature16468

Reimer, J., Froudarakis, E., Cadwell, C. R., Yatsenko, D., Denfield, G. H., & Tolias, A. S. (2014). Pupil fluctuations track fast switching of cortical states during quiet wakefulness. Neuron, 84(2), 355-362. doi:10.1016/j.neuron.2014.09.033

Froudarakis, E., Berens, P., Ecker, A. S., Cotton, R. J., Sinz, F. H., Yatsenko, D., Saggau, P., Bethge, M. & Tolias, A. S. (2014). Population code in mouse V1 facilitates readout of natural scenes through increased sparseness. Nature neuroscience, 17(6), 851-857. doi:10.1038/nn.3707

Cotton, R. J., Froudarakis, E., Storer, P., Saggau, P., & Tolias, A. S. (2013). Three-dimensional mapping of microcircuit correlation structure. Frontiers in neural circuits, 7, 151.

Note that this is a subset of the data reported in Theis et al. (2016). The other subset has been set aside to serve as test set in a spike inference competition and will be released once the competition is finished. The training set of the competition will be identical to the dataset released here.

Format of the data

The data from each experiment is provided as a Matlab file (.mat) and a Python pickle file (.pck). Details of the data format are given in the document linked to at the bottom of this page. Total size of the data is about 40MB (compressed).

Conditions for usage of this data in publications

If you publish any work using the data, please cite the first publication listed above (Theis et al. 2016) and also cite the data set in the following recommended format:

Berens, P., Theis, L., Froudarakis, E., Reimer, J., Rosón, M. R., Baden, T., Euler T., Tolias, A.S. & Bethge, M. (2016); Simultaneous two-photon imaging and electrophysiological recordings from neurons in the mouse retina and primary visual cortex using OGB and GCamp6.

The above citation uses a Digital Object Identifier (DOI) which is assigned to the data set.  The DOI was created using DataCite ( and the California Digital Library, "EZID" system (

How to download the data

Data may be downloaded from:
A account is required. See the download link for more instructions.

Getting help using the data

If you have questions about using the data, please post them on the forum for using data sets.

Documentation file

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