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Notebooks for Behrens et al.

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Notebooks for Behrens et al.

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Notebooks for Behrens, Schubert, Haverkamp, Euler and Berens: 

## Connectivity map of bipolar cells and photoreceptors in the mouse retina

Published as [Behrens, Schubert et al., eLife, 2016, e20041](https://elifesciences.org/content/5/e20041)

*Abstract*: In the mouse retina, three different types of photoreceptors provide input to 14 bipolar cell (BC) types. Classically, most BC types are thought to contact all cones within their dendritic field; ON-BCs would contact cones exclusively via so-called invaginating synapses, while OFF-BCs would form basal synapses. By mining publically available electron microscopy data, we discovered interesting violations of these rules of outer retinal connectivity: ON-BC type X contacted only ~20% of the cones in its dendritic field and made mostly atypical non-invaginating contacts. Types 5T, 5O and 8 also contacted fewer cones than expected. In addition, we found that rod BCs received input from cones, providing anatomical evidence that rod and cone pathways are interconnected in both directions. This suggests that the organization of the outer plexiform layer is more complex than classically thought.

### Figure 1

- [Cone overview projections (C&D, also Fig. 3E, Fig. 3 Supp 2A, Fig. 4B)](./cone_overview_projection.ipynb)
- [S-cone classification (E)](./S_cone_classification.ipynb)
- [Classification of CBC5 subtypes](./CBC5_classification.ipynb)

### Figure 2

- [Analysis of the contact points between cone pedicles and bipolar cell dendrites](./cone_contact_analysis.ipynb)
- [Classification of the contacts (D-I, table 1)](./cone_contact_classification.ipynb)

### Figure 3

- [Evaluation of the contact statistics (B&D, also Fig. 3 Supp 2B&C)](./cone_contact_evaluation.ipynb)
- [Dendritic field size and coverage factors of BC (F&G)](./dendritic_field_and_cone_coverage.ipynb)
- [Calculation of contact densities for bipolar cell types (H&I)](./BC_contact_density.ipynb) 

### Figure 4
- [Comparison of contacts between cone contacts of CBCXs and other ON-CBC types (D)](./CBCX_ON_CBC_contact_comparison.ipynb)
- [Comparison of the contact area of basal contacts between CBCXs and OFF-CBCs (D)](./CBCX_OFF_CBC_contact_area_comparison.ipynb)

### Figure 5
- [Statistics of contacts between RBC and cones (C-E)](./cone_contact_evaluation.ipynb)
- [Analysis of possible RBC subtypes (Supp. 2)](./RBC_subtypes.ipynb)

### Figure 6
- [Analysis of the contact points between rod spherules and bipolar cell dendrites](./rod_contact_analysis.ipynb)
- [Classification of the contacts (Supp. 1, table 2)](./rod_contact_classification.ipynb)
- [Evaluation of the contact statistics (D-F)](./rod_contact_evaluation.ipynb)

### Table 3
- [Calculation of coverage factors from convex hulls](./coverage_factors.ipynb)
- [Calculation of coverage factors from cones](./dendritic_field_and_cone_coverage.ipynb) 

If you have any questions, please contact [Philipp Berens](mailto:philipp.berens@uni-tuebingen.de). We thank Moritz Helmstaedter and colleagues for making their [data and code](http://www.neuro.mpg.de/connectomics) available.


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