(q)_(p)
\ . . / Quick
=\ t /= Curate
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A quick-fire, text-based curation tool which uses spikeinterface report folders.
Can either be used in Jupyter or Kitty.
Using terminal, activate your virtual enviroment and navigate to where you like to keep your git repos (cd path/to/my/git/folders). In that folder, run
git clone https://github.com/chrishalcrow/quickcurate.git
cd quickcurate
pip install .If you're using Kitty, you may also need to do this:
export MPLBACKEND='module://matplotlib-backend-kitty'which adds the matplotlib backend to kitty; or the kitty frontend to matplotlib; or something like that.
Open jupyter, and run
from quickcurate import curate
curation_dict = curate(
labels=["good", "bad", "noise"], # or whichever labels you'd like
report_folder = "path/to/folder/" # where your report is saved
output_file = "where_to_save_the_curation_dict.json" # Optional
)The output, curation_dict, is a dictionary of labels e.g. curation_dict = {0: 'good', 1: 'good', 2: 'noise', ...}. Alternatively, the labels can be found where you have saved output_file.
Open your Kitty terminal, and run
quickcurate "path/to/spikeinterface/report/folder"By default, your curation is saved in the report folder. You can specify somewhere else to save it as follows:
quickcurate "report_folder" --output_file "my_output_folder/my_curation.json"Spikeinterface is spike-sorting software for ephys data. It has a great export_report function, which generates a summary of your sorted data. You often want to curate this data: which units are single-neuron units, which are noise etc. To do this you often need intricate, interactive tools such as phy, sortingview or spikeinterfacegui. Occassioanlly, you only need the simple stuff contained in the report. In this case quickcurate is your friend.