Datasets¶
Drosophila larval mushroom body¶
- graspologic.datasets.load_drosophila_left(return_labels=False)[source]¶
Load the left Drosophila larva mushroom body connectome
The mushroom body is a learning and memory center in the fly brain which is involved in sensory integration and processing. This connectome was observed by electron microscopy and then individial neurons were reconstructed; synaptic partnerships between these neurons became the edges of the graph.
- Parameters:
- return_labelsbool, optional (default=False)
whether to have a second return value which is an array of cell type labels for each node in the adjacency matrix
- Returns:
- graphnp.ndarray
Adjacency matrix of the connectome
- labelsnp.ndarray
Only returned if
return_labelsis true. Array of string labels for each cell (vertex)
- Parameters:
return_labels (bool) --
- Return type:
ndarray | Tuple[ndarray, ndarray]
References
[1]Eichler, K., Li, F., Litwin-Kumar, A., Park, Y., Andrade, I., Schneider-Mizell, C. M., ... & Fetter, R. D. (2017). The complete connectome of a learning and memory centre in an insect brain. Nature, 548(7666), 175.
- graspologic.datasets.load_drosophila_right(return_labels=False)[source]¶
Load the right Drosophila larva mushroom body connectome
The mushroom body is a learning and memory center in the fly brain which is involved in sensory integration and processing. This connectome was observed by electron microscopy and then individial neurons were reconstructed; synaptic partnerships between these neurons became the edges of the graph.
- Parameters:
- return_labelsbool, optional (default=False)
whether to have a second return value which is an array of cell type labels for each node in the adjacency matrix
- Returns:
- graphnp.ndarray
Adjacency matrix of the connectome
- labelsnp.ndarray
Only returned if
return_labelsis true. Array of string labels for each cell (vertex)
- Parameters:
return_labels (bool) --
- Return type:
ndarray | Tuple[ndarray, ndarray]
References
[1]Eichler, K., Li, F., Litwin-Kumar, A., Park, Y., Andrade, I., Schneider-Mizell, C. M., ... & Fetter, R. D. (2017). The complete connectome of a learning and memory centre in an insect brain. Nature, 548(7666), 175.
Duke mouse whole-brain connectomes¶
- graspologic.datasets.load_mice()[source]¶
Load connectomes of mice from distinct genotypes.
Dataset of 32 mouse connectomes derived from whole-brain diffusion magnetic resonance imaging of four distinct mouse genotypes: BTBR T+ Itpr3tf/J (BTBR), C57BL/6J(B6), CAST/EiJ (CAST), and DBA/2J (DBA2). For each strain, connectomes were generated from eight age-matched mice (N = 8 per strain), with a sex distribution of four males and four females. Each connectome was parcellated using asymmetric Waxholm Space, yielding a vertex set with a total of 332 regions of interest (ROIs) symmetrically distributed across the left and right hemispheres. Within a given hemisphere, there are seven superstructures consisting up multiple ROIs, resulting in a total of 14 distinct communities in each connectome.
- Returns:
- data
Bunch Dictionary-like object, with the following attributes.
- graphslist of np.ndarray
List of adjacency matrices of the connectome
- labelsnp.ndarray
Array of string labels for each mouse (subject)
- atlaspd.DataFrame
DataFrame of information for each ROI
- blockspd.DataFrame
DataFrame of block assignments for each ROI
- featurespd.DataFrame
DataFrame of anatomical features for each ROI in each connectome
- participantspd.DataFrame
DataFrame of subject IDs and genotypes for each connectome
- metaDictionary
Dictionary with meta information about the dataset (n_subjects and n_vertices)
- data
- Return type:
References
[1]Wang, N., Anderson, R. J., Ashbrook, D. G., Gopalakrishnan, V., Park, Y., Priebe, C. E., ... & Johnson, G. A. (2020). Variability and heritability of mouse brain structure: Microscopic MRI atlases and connectomes for diverse strains. NeuroImage. https://doi.org/10.1016/j.neuroimage.2020.117274