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Data from: Spectral inference reveals principal cone-integration rules of the zebrafish inner retina

Cite this dataset

Baden, Tom; Bartel, Philipp; Yoshimatsu, Takeshi; Janiak, Filip K (2021). Data from: Spectral inference reveals principal cone-integration rules of the zebrafish inner retina [Dataset]. Dryad.


In the vertebrate retina, bipolar cells integrate the signals from different cone types at two main sites: directly, via dendritic inputs in the outer retina, and indirectly, via axonal inputs in the inner retina. Of these, the functional wiring of the indirect route, involving diverse amacrine cell circuits, remains largely uncharted. However, because cone-photoreceptor types differ in their spectral sensitivities, insights into the total functional cone-integration logic of bipolar cell might be gained by linking spectral responses across these two populations of neurons. To explore the feasibility of such a “spectral-circuit-mapping” approach, we here recorded in vivo responses of bipolar cell presynaptic terminals in larval zebrafish to widefield but spectrally resolved flashes of light. We then mapped the results onto the previously established spectral sensitivity functions of the four cones.

We find that this approach could explain ∼95% of the spectral and temporal variance of bipolar cell responses by way of a simple linear model that combined weighted inputs from the cones with four stereotyped temporal components. This in turn revealed several notable integration rules of the inner retina. Overall, bipolar cells were dominated by red-cone inputs, often alongside equal sign inputs from blue- and green-cones. In contrast, UV-cone inputs were uncorrelated with those of the remaining cones. This led to a new axis of spectral opponency which was mainly set-up by red-/green-/blue-cone “Off” circuits connecting to “natively-On” UV-cone circuits in the outermost fraction of the inner plexiform layer – much as how key colour opponent circuits are established in mammals. Beyond this, and despite substantial temporal diversity that was not present in the cones, bipolar cell spectral tunings were surprisingly simple. They either approximately resembled both opponent and non-opponent spectral motifs already present in the cones or exhibited a stereotyped non-opponent broadband response. In this way, bipolar cells not only preserved the efficient spectral representations in the cones, but also diversified them to set up a total of six dominant spectral motifs which included three axes of spectral opponency. More generally, our results contribute to an emerging understanding of how retinal circuits for colour vision in ancestral cone-tetrachromats such as zebrafish may be linked to those found in mammals.


2P imaging of retinal bipolar cells in larval zebrafish, stimulated with widefield but spectrally narrow flashes of light. For full details, please see the methods in the associate manuscript.

Usage notes

All preprocessed data is contained in the two csv files.

In addition, we provide all key processed data panels as shown in the paper as IgorPro format. There are contaoined in the big zip folder.

To read these, go to and download a free trial version of Igor (valid 1 month). Opening each file will then bring up the relevant data panel as plotted in the MS. The data therein can be looked at via the "Data Browser" option. From here, the data can also be exported into any common format (delimited text, hd5 etc. as needed).


Wellcome Trust, Award: 220277/Z20/Z

European Research Council, Award: 677687

Biotechnology and Biological Sciences Research Council, Award: BB/R014817/1

Leverhulme Trust, Award: PLP-2017-005 and RPG-2021-026

Lister Institute of Preventive Medicine, Award: Fellowship to TB