From 39f2b11175fb872a6748f5cb6b0245373b28d493 Mon Sep 17 00:00:00 2001 From: zm711 <92116279+zm711@users.noreply.github.com> Date: Fri, 15 Sep 2023 16:45:05 -0400 Subject: [PATCH 1/2] Update README.md --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 8c0e07e..b616210 100644 --- a/README.md +++ b/README.md @@ -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!). @@ -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( @@ -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) ``` @@ -97,7 +97,7 @@ sigui /path/for/my/waveforms ## Install -You need first to install one of these 3 packages (by order of preference): +You need first to install **one** of these 3 packages (by order of preference): * `pip install PySide6` * `pip install PyQt6` * `pip install PyQt5` From efe723e546a053a78588c2e5ba7713dfbd1d3c43 Mon Sep 17 00:00:00 2001 From: Zach McKenzie <92116279+zm711@users.noreply.github.com> Date: Sat, 16 Sep 2023 19:17:14 -0400 Subject: [PATCH 2/2] add link to installation instructions --- README.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index b616210..09efeb3 100644 --- a/README.md +++ b/README.md @@ -97,12 +97,17 @@ sigui /path/for/my/waveforms ## Install +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` - * `pip install PyQt6` + * `pip install PySide6` or + * `pip install PyQt6` or * `pip install PyQt5` - From pypi: ```bash