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exporting to phy for manual curation #3436
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Hey @kshtjkumar, which version of spikeinterface are you using? You should be to reload your data either as a waveform extractor (version < 0.101.0) or sorting analyzer (version >= 0.101.0) and then use the export_to_phy. we also offer manual curation through the spikeinterface-gui as well as through sortingview. |
i am currently using 0.100.6 version, can you help on how to load it in phy or spikeinterface GUI ? |
Could you post your script for analyzing your data? Basically you just need your waveform extractor and that can be used as an input to |
I used mountainsort 5 to sort the data using scheme 2. The waveform folder of each recording has these file :
|
For spikeinterface-gui you need a sorting analyzer. The easiest way is to use spikeinterface 0.101.0 and this from spikeinterface.widgets import plot_sorting_summary
plot_sorting_summary(sorting_analyzer, curation=True, backend="spikeinterface_gui") |
@zm711 ? |
Hi, so i created a new environment installing 0.101.0. Now i tried the codes on this: https://github.com/SpikeInterface/spikeinterface-gui is it possible to do any of this based on the pre sorted recordings ? i have a folder called waveforms from each recording generated after sorting and the files in it are the same that i mentioned above. Could you please give a clarity on if the manual sorting is possible based on these files or do i resort every file again ! |
Well there are two components to this. You would never need to "resort" between version. If you are okay with the sorting results we have various I think what you worried about is if the waveform extractor data will still be useful and it is. We have a backward compatibility function just for this case. Do you want to read the docs on it and then if you have more questions let us know! Once you've converted your waveform extractor into a sorting analyzer you'll be able to use the spikeinterface-gui :) |
hi @zm711, this was really helpful, i used spikeinterface 0.100.6 and ran the following, it worked perfectly:
this opens perfectly in phy (but ofc not in spikeinterface gui!) and now am having trouble with understanding phy. |
@zm711 |
What was the previous version? |
for all the analysis the version used is/was 0.100.6 @alejoe91 |
@alejoe91 i tried reinstalling but same error persists! Please suggest how to fix this ? |
@zm711 hi, sorry to bother again, but could you please help here! A lot is stuck due to this. |
Sorry @kshtjkumar I had a presentation at work so was off of SI/github issues. I need to get re-oriented. So you basically did your analysis with 100.6 so with a waveform extractor. could you show us the contents of your waveform folder/ share your json files in that folder. did you move anything (for example from a server to local or vice versa?). Best case scenario you share the json here. Second best would be you share edited for privacy json files. |
waveforms_kshtj_961_aug_2023_lko_230801_151701347713.zip |
So this says the file was originally on your E drive, but you moved it to your c drive for this. inside the |
hi @zm711 this works perfectly! I shifted my waveform folder to E drive and everthing gets loaded!
I hope this approach is correct ! |
Hi,
I’ve run spike sorting for several files and have the corresponding waveforms stored. Below is the code I used to display the folder contents:
this is the output:
I have several such folders, and I’d like to perform manual curation since the waveforms and SNR are good, but the ISI ratio is high. I’m still new to manual curation, so any resources or guidance would be appreciated.
Is it possible to load the existing results and convert them to
export_to_phy
? I’d prefer not to rerun the spike sorting for each file, as it’s time-consuming. What would be the best way to approach this?Thanks!
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