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.

The mouse retina contains a single type of horizontal cell, a GABAergic interneuron that samples from all cone photoreceptors within reach and modulates their glutamatergic output via parallel feedback mechanisms. Because horizontal cells form an electrically coupled network, they have been implicated in global signal processing, such as large-scale contrast enhancement. Recently, it has been proposed that horizontal cells can also act locally at the level of individual cone photoreceptors. To test this possibility physiologically, we used two-photon microscopy to record light stimulus-evoked Ca signals in cone axon terminals and horizontal cell dendrites as well as glutamate release in the outer plexiform layer. By selectively stimulating the two mouse cone opsins with green and UV light, we assessed whether signals from individual cones remain isolated within horizontal cell dendritic tips or whether they spread across the dendritic arbor. Consistent with the mouse's opsin expression gradient, we found that the Ca signals recorded from dendrites of dorsal horizontal cells were dominated by M-opsin and those of ventral horizontal cells by S-opsin activation. The signals measured in neighboring horizontal cell dendritic tips varied markedly in their chromatic preference, arguing against global processing. Rather, our experimental data and results from biophysically realistic modeling support the idea that horizontal cells can process cone input locally, extending the classical view of horizontal cell function. Pharmacologically removing horizontal cells from the circuitry reduced the sensitivity of the cone signal to low frequencies, suggesting that local horizontal cell feedback shapes the temporal properties of cone output.

The retina decomposes visual stimuli into parallel channels that encode different features of the visual environment. Central to this computation is the synaptic processing in a dense layer of neuropil, the so-called inner plexiform layer (IPL). Here, different types of bipolar cells stratifying at distinct depths relay the excitatory feedforward drive from photoreceptors to amacrine and ganglion cells. Current experimental techniques for studying processing in the IPL do not allow imaging the entire IPL simultaneously in the intact tissue. Here, we extend a two-photon microscope with an electrically tunable lens allowing us to obtain optical vertical slices of the IPL, which provide a complete picture of the response diversity of bipolar cells at a "single glance". The nature of these axial recordings additionally allowed us to isolate and investigate batch effects, i.e. inter-experimental variations resulting in systematic differences in response speed. As a proof of principle, we developed a simple model that disentangles biological from experimental causes of variability and allowed us to recover the characteristic gradient of response speeds across the IPL with higher precision than before. Our new framework will make it possible to study the computations performed in the central synaptic layer of the retina more efficiently. The primary excitatory pathway of the mouse retina consists of photoreceptors, bipolar cells (BCs) and retinal ganglion cells (RGCs) (reviewed in refs. 1,2). At the core of this pathway is the inner plexiform layer (IPL), a dense synaptic plexus composed of the axon terminals of BCs, the neurites of amacrine cells, as well as the dendrites of RGCs. Specifically, the photoreceptor signal is relayed by the BCs to the RGCs via glutamatergic synapses (reviewed in ref. 3). This "vertical" transmission is shaped by mostly inhibitory interactions with amacrine cells, which integrate signals laterally along and/or vertically across the IPL (reviewed in ref. 4). Amacrine cells modulate, for instance, the sensitivity of BCs to certain spatio-temporal features 5-7. Within the IPL, the axon terminals of each of the 14 BC types 8-12 project to a distinct depth with axonal profiles of different BC types partially overlapping and jointly covering the whole depth of the IPL 10,11,13. Functionally, each BC type constitutes a particular feature channel, with certain temporal dynamics 7 , including On and Off BC types sensitive to light increments or decrements, respectively 14 , different kinetics 15,16 , and chromatic signals 17,18. Some of these features are systematically mapped across the IPL: For example, On BCs project to the inner and Off BCs to the outer portion of the IPL 14,19. Also kinetic response properties appear to be mapped, with the axonal profiles of more transient BCs localised in the IPL centre 7,15,20,21. To study BC function, early studies mostly used single-cell electrical recordings in vertical slices, where many lateral connections (e.g. large-scale amacrine cells) are severed, o...