msa
Script to process miniscope data and quantify activity (e.g. spontaneous peaks and correlations) on arbitrary epoch definitions.
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary
Repository
Script to process miniscope data and quantify activity (e.g. spontaneous peaks and correlations) on arbitrary epoch definitions.
Basic Info
- Host: GitHub
- Owner: leomol
- License: gpl-3.0
- Language: MATLAB
- Default Branch: master
- Size: 4.91 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Single unit analisis
Script to process single unit data and quantify activity (e.g. spontaneous peaks and correlations) on arbitrary epoch definitions.
Installation
- Download and install MATLAB.
- Download and extract source files to
Documents/MATLAB - For analyses involving deconvolution of CA²⁺ data, download and implement such library in the code. For example, download OASIS library, run
oasis_setup.m, and use one of the examples under examples.
Usage
- Run
setup.mto add FPA dependencies to the MATLAB search path. - Create a copy of the example script.
- Change the configuration variables and the data loader according to your data acquisition system.
- Define epochs.
- Change settings and thresholds to compute peaks and clusters.
- Click
Run.
Epochs consists of an array of timestamps indicating start and stop times (in seconds) of a given condition {'epoch1', [start1, end1, start2, end2, ...], 'epoch2', ...}. For example:
MATLAB
epochs = {'A', [100, 200], 'B', [200, 500], 'C', [500, 600, 600, 700]};
means there are three epochs called A, B, and C:
A: 100 to 200
B: 200 to 500
C: 500 to 600 then 600 to 700
Documentation
msa = MSA(data, configuration);
Normalize, filter, and detect peaks of spontaneous activity in user defined epochs.
Each column in data corresponds to activity from individual cells.
configuration is a struct with the following fields (defaults are used for missing fields):
- conditionEpochs - Epochs for different conditions: {'epoch1', [start1, end1, start2, end2, ...], 'epoch2', ...}
- thresholdEpochs - Epochs to include for peak threshold calculation.
- events - Event-triggered data; times at which a type of event occurs.
- resamplingFrequency - Resampling frequency (Hz).
- lowpassFrequency - Lowest frequency permitted in normalized signal.
- peakSeparation - Minimum time separation between two peaks.
Processing steps
- Resample signal and reference to a given frequency.
- Baseline correction modeled as an exponential decay of the low-pass filtered data (optionally using airPLS).
- Correct for motion artifacts by subtracting reference to signal, after a polynomial fit (optional).
- Remove fast oscillations with a low-pass filter.
- Normalize data as df/f or z-score according to settings.
- Find peaks of spontaneous activity in low-pass filtered data.
Normalization is calculated as (f - f0) / f1 where f0 and f1 can be data provided by the user or calculated using given functions:
See examples and source code for detailed analysis steps and default parameters. Units for time and frequency are seconds and hertz respectively.
License
© 2019 Leonardo Molina
This project is licensed under the GNU GPLv3 License.
Owner
- Name: Leo
- Login: leomol
- Kind: user
- Repositories: 5
- Profile: https://github.com/leomol
Citation (CITATION.cff)
cff-version: 1.2.0
title: "Miniscope analysis toolbox"
abstract: "MATLAB toolbox to process multi-unit calcium signals."
message: If you use this software, please cite it.
type: software
version: 1.0.0
date-released: 2019-07-31
repository-code: https://github.com/leomol/MSA
authors:
- family-names: "Molina"
given-names: "Leonardo A."
email: "leonardomt@gmail.com"
affiliation: "University of Calgary"
orcid: https://orcid.org/0000-0002-6601-7185
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0