worm-functional-connectivity
Functional connectivity atlas for the C. elegans brain
Author: Francesco Randi francesco.randi@gmail.com
Installation
-
Install from GitHub
python -m pip install git+https://github.com/leiferlab/worm-functional-connectivity
Usage
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The main class in the python module is
FunctionalAtlas
.-
Use the
FunctionalAtlas.from_file()
method to load a pickled instance from file. -
There are docstrings and comments for documentation.
-
The class has two main methods:
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get_standard_stimulus()
to generate one of the standard stimuli from the parameters chosen by the user. -
get_responses()
that returns the responses that need to be plotted. The methodget_responses()
expects a stimulus (e.g. generated byget_standard_stimulus()
) and either a list of neuron IDs whose response the user wants to plot, or a threshold to ask for all the responses above that threshold. See the docstring for any temporary behavior for this mock atlas.
-
-
Command line utilities
use_mock_atlas_scalar
- Uses the mock functional atlas stored inatlas/mock.pickle
to generate a scalar version of the functional connectivity matrix.
usage: use_mock_atlas_scalar [-h] [--mode MODE]
[--amplitude-threshold THRESHOLD]
[--matrix-output FILE] [--pairwise-output FILE]
[-p] [-v]
Use the mock atlas and return a scalar version of the functional connectivity
matrix (amplitude, timescales, or other)
optional arguments:
-h, --help show this help message and exit
--mode MODE Type of scalar quantity to extract from functional
connectivity. Can be amplitude or timescales.
--amplitude-threshold THRESHOLD
Amplitude values below the threshold will be set to
zero.
--matrix-output FILE Save the matrix to a tab delimited file
--pairwise-output FILE
Save the matrix with one line per neuron pair in a tab
delimited file
-p, --show-plot Plot output
-v, --verbose increase output verbosity
As an alternative to the commandline, params can be placed in a file, one per
line, and specified on the commandline like 'use_mock_atlas_scalar
@params.conf'.
Example scripts
-
scripts/generate_mock_atlas.py
- Example showing how to generate a mock functional connectivity atlas. -
scripts/use_mock_atlas.py
- Example of how to generate a stimulus usingFunctionalAtlas.get_standard_stimulus()
and then provide that stimulus toFunctionAtlas.get_responses()
to get the neuronal responses to that stiumuls.