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gridcell's Introduction

gridcell

Package to facilitate the analysis of the spatial modulation of neuronal activity, based on spike train recordings from neurons during animal behavior. The package is primarily focused on analyzing grid cells.

The package is made available under the Apache License Version 2.0.

Copyright 2015 Daniel Wennberg

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gridcell's Issues

Basic grid cell analysis functionality

Currently the package is made with the assumption that it will be used on cells that have already been identified as grid cells. A natural next step would be to implement a grid score method in the Cell class, and implement a test identifying grid cells based on some grid score criteria, shuffling etc.

Another thing to consider implementing is kernel smoothed density estimation in the CellCollection class, to inform the clustering of cells into modules (e.g. to determine the n_clusters parameter for K-means clustering).

Tests

The package has grown to a considerable size, and should get its own test suite. The ad-hoc method of writing notebooks and looking at the output is no longer sufficient.

Factor away plotting methods

Having a bunch of plotting methods on the objects is making them heavy and bloated. All plotting functionality should be factored out into a separate module with plotting functions taking as arguments instances of classes for which plotting is relevant. This should be a flexible and general-purpose module, not an opinionated, seaborn-dependent and option-deprived module like 'niceplots'.

Docstring formatting

The docstrings are poorly formatted and should be rewritten according to the numpy docstring standard. But... ain't nobody got time for that!

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