hana: high density micro electrode array recordings analysis

Hana is a Python library for analysing recordings made by the "hidens" high density micro electrode arrays.

If you use this library in your research, please cite our paper (Frontiers):

Bullmann T, Radivojevic M, Huber S, Deligkaris K, Hierlemann A, Frey U (2019) Large-scale mapping of axonal arbors using high-density microelectrode arrays. Accepted

@article {Bullmann2019b,
	author = {Torsten Bullmann, Milos Radivojevic, Stefan Huber, Kosmas Deligkaris, Andreas Reinhold Hierlemann, Urs Frey},
	title = {Large-scale mapping of axonal arbors using high-density microelectrode arrays},
	year = {2019},
	doi = {},
	URL = {},
	eprint = {},
	journal = {Frontiers in Cellular Neuroscience, section Cellular Neurophysiology}
}

Requirements

Hana requires Python 2.7 to run, but might be compatible to Pyhton 3.5. For a full list of dependencies, see the requirements.txt file. An example conda environment can be found in the environment.yaml file

Installation

See installation instruction for the hdmea_axons package.

Usage

1. hdmea_axon.
2. hdmea_network.

Components

Main functionality

• Accessing data
• Segmenation of axons and dendrites
• Estimation of structural connectivity
• Estimation of functional connectivity and some tests
• Detection of polychronous groups

Supporting

• Miscellaneous
• General plotting functions
• Hexagonal grid conversions
• HDF5 for dictionaries

Acknowledgement

The h4dict code was posted by a unknown user hjpaul on stackexchange, and the original can be found here