netneurotools.datasets.fetch_famous_gmat

netneurotools.datasets.fetch_famous_gmat(dataset, force=False, data_dir=None, verbose=1)

Download files from multi-species connectomes.

This dataset contains

If you used this data, please cite celegans [1], drosophila [2], human [3], macaque_markov [4], macaque_modha [5], mouse [6], rat [7].

Parameters:

dataset (str) – Specifies which dataset to download.

Returns:

data – Dictionary-like object with, at a minimum, keys [‘conn’, ‘labels’, ‘ref’] providing connectivity / correlation matrix, region labels, and relevant reference. Other possible keys include ‘dist’ (an array of Euclidean distances between regions of ‘conn’), ‘coords’ (an array of xyz coordinates for regions of ‘conn’), ‘acronyms’ (an array of acronyms for regions of ‘conn’), and ‘networks’ (an array of network affiliations for regions of ‘conn’).

Return type:

sklearn.utils.Bunch

Other Parameters:

• force (bool, optional) – If True, will overwrite existing dataset. Default: False

• data_dir (str, optional) – Path to use as data directory. If not specified, will check for environmental variable ‘NNT_DATA’; if that is not set, will use ~/nnt-data instead. Default: None

• verbose (int, optional) – Modifies verbosity of download, where higher numbers mean more updates. Default: 1

References

[1]

Lav R Varshney, Beth L Chen, Eric Paniagua, David H Hall, and Dmitri B Chklovskii. Structural properties of the caenorhabditis elegans neuronal network. PLoS computational biology, 7(2):e1001066, 2011.

[2]

Ann-Shyn Chiang, Chih-Yung Lin, Chao-Chun Chuang, Hsiu-Ming Chang, Chang-Huain Hsieh, Chang-Wei Yeh, Chi-Tin Shih, Jian-Jheng Wu, Guo-Tzau Wang, Yung-Chang Chen, and others. Three-dimensional reconstruction of brain-wide wiring networks in drosophila at single-cell resolution. Current biology, 21(1):1–11, 2011.

[3]

Alessandra Griffa, Yasser Alemán-Gómez, and Patric Hagmann. Structural and functional connectome from 70 young healthy adults [data set]. Zenodo, 2019.

[4]

Nikola T Markov, Maria Ercsey-Ravasz, Camille Lamy, Ana Rita Ribeiro Gomes, Loïc Magrou, Pierre Misery, Pascale Giroud, Pascal Barone, Colette Dehay, Zoltán Toroczkai, and others. The role of long-range connections on the specificity of the macaque interareal cortical network. Proceedings of the National Academy of Sciences, 110(13):5187–5192, 2013.

[5]

Dharmendra S Modha and Raghavendra Singh. Network architecture of the long-distance pathways in the macaque brain. Proceedings of the National Academy of Sciences, 107(30):13485–13490, 2010.

[6]

Mikail Rubinov, Rolf JF Ypma, Charles Watson, and Edward T Bullmore. Wiring cost and topological participation of the mouse brain connectome. Proceedings of the National Academy of Sciences, 112(32):10032–10037, 2015.

[7]

Mihail Bota, Olaf Sporns, and Larry W Swanson. Architecture of the cerebral cortical association connectome underlying cognition. Proceedings of the National Academy of Sciences, 112(16):E2093–E2101, 2015.