Skip to content

Commit

Permalink
Merge pull request #50 from zm711/main
Browse files Browse the repository at this point in the history
Fix missing parenthesis and add edits for clarity
  • Loading branch information
samuelgarcia authored Sep 18, 2023
2 parents 0f81216 + efe723e commit 385d51d
Showing 1 changed file with 14 additions and 9 deletions.
23 changes: 14 additions & 9 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ and quality of any spike sorter supported by spikeinterface
This interactive GUI offer several views that dynamically refresh other views.
This allows us to very quickly check the strengths and weaknesses of any sorter output.

Contrary to other viewers (like phy), this viewer skips the tedious and long step of
copying and reformating the entire dataset (filtered signal + waveform + PCA) to a particular
Contrary to other viewers (like phy), this viewer skips the tedious and long step of
copying and reformatting the entire dataset (filtered signal + waveform + PCA) to a particular
format or folder organisation. This gui is built on top of spikeinterface objects
(Recording, Sorting, WaveformExtractor)
These objects are "lazy" and retrieve data on the fly (no copy!).
Expand Down Expand Up @@ -47,7 +47,7 @@ recording_filtered = si.bandpass_filter(recording)
sorting = si.run_sorter('YYYYY', recording_filtered)

# extract waveforms
# sparse is important because make everything faster!!!
# sparsity is important because it makes everything faster!!!
waveform_folder = '/path/for/my/waveforms'
job_kwargs = dict(n_jobs=10, chunk_duration='1s', progress_bar=True,)
we = si.extract_waveforms(
Expand All @@ -62,12 +62,12 @@ si.compute_noise_levels(we)

# optionally compute more stuff using the spikeinterface.postprocessing module
# principal components, template similarity, spike amplitudes
# This will enable to display more views
# This will enable us to display more views
si.compute_principal_components(we,
n_components=3,
mode='by_channel_local',
whiten=True)
si.compute_template_similarity(we, method='cosine_similarity',
si.compute_template_similarity(we, method='cosine_similarity')
si.compute_spike_amplitudes(we, **job_kwargs)
```

Expand Down Expand Up @@ -97,11 +97,16 @@ sigui /path/for/my/waveforms

## Install

You need first to install one of these 3 packages (by order of preference):
* `pip install PySide6`
* `pip install PyQt6`
* `pip install PyQt5`
For beginners or Anaconda users please see our [installation tips](https://github.com/SpikeInterface/spikeinterface/tree/main/installation_tips)
where we provide a yaml for Mac/Windows/Linux to help properly install `spikeinterface` and `spikeinterface-gui` for you in a dedicated
conda environment.

Otherwise,

You need first to install **one** of these 3 packages (by order of preference):
* `pip install PySide6` or
* `pip install PyQt6` or
* `pip install PyQt5`

From pypi:

Expand Down

0 comments on commit 385d51d

Please sign in to comment.