This project aims to provide various utilities for multi-electrode array recording setups based on MWorks (http://mworks-project.org/) and Blackrock/Plexon systems.
To install:
python setup.py install
To install locally under the home directory:
python setup.py install --user
Note that the package depends on the following Python packages:
- numpy
- scipy
- pytables
- scikit-learn
- pywt
- joblib
- pymworks (https://github.com/hahong/pymworks.git)
- pymario (https://github.com/hahong/pymario.git)
Core utilities and a typical procedure:
+--------+ +------------------+
| MWorks | | BlackRock/Plexon |
+--------+ +------------------+
| |
v v
(Original .mwk) (.nev/.plx)------------+
| | |
v v |
+-----------------------------------------------+ |
| maru-merge: merge behavior .mwk files and | |
| neural signal files .nev/.plx to produce | |
| merged .mwk files | |
+---------------------+-------------------------+ |
| |
v |
+-------- (Merged .mwk files) |
| | |
| . .
| . .
| . (Optional: spike sorting) .
| . .
| . .
| v v
| +-----------------------------------------------+
| | maru-psinfo --wav=<.nev file name> |
| | collect peristimulus spike information AND |
| | waveform snippets of the spikes |
| +----------------------+------------------------+
| |
| v
| (Peristimulus spiking information w/ waveforms)
| |
| v
| +-----------------------------------------------+
| | maru-spksort feature |
| | compute features for clustering |
| +----------------------+------------------------+
| |
| v
| (Feature files.c1.feat.h5)
| |
| v
| +-----------------------------------------------+
| | maru-spksort cluster |
| | sort spikes by clustering |
| +----------------------+------------------------+
| |
| v
| (Sorted spikes files.c2.clu.h5)
| |
| v
| +-----------------------------------------------+
| | maru-spksort collate |
| | merge multiple .c2.clu.h5 files and produce |
| | peristimulus spike information.psf.h5 files |
| +---------------------------------+-------------+
| |
v |
+-----------------------------------+ |
| maru-psinfo: collect peristimulus | |
| spike information without | |
| spike sorting | |
+-------------------+---------------+ |
| |
v v
(Peristimulus spiking information.psf.h5)
|
v
+-----------------------------------------------+
| maru-util-psinfo2feat: compute feature matrix |
| by integrating over time bins |
+----------------------+------------------------+
|
v
(Features.feat.h5)
|
v
+-----------------------------------------------+
| maru-util-featconcat: concatnate multiple |
| feature matrix files into a single file |
+----------------------+------------------------+
|
v
(Concatenated features.feat.h5)
Additional utilities:
- maru-check-psth: plot PSTHs for .psf.h5 files and provide diagnosis about the quality of the channels.
- maru-check-impedance: compare multiple BlackRock impedance log files and visualize changes.