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flatironinstitute / ironclust

Spike sorting software being developed at Flatiron Institute, based on JRCLUST (Janelia Rocket Cluster)
Apache License 2.0
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How to use The feature-vs-time view (Time vs. Amplitude)? #30

Open kouichi-c-nakamura opened 5 years ago

kouichi-c-nakamura commented 5 years ago

I'm reading this for a while but it seems documentation lacks some information.

figtime

Let me ask a few questions about the window.

  1. What is the red rectangle for? I initially thought that this is to be dragged so that the user can set a threshold for splitting. However, splitting actually adds another polygon. If they are both for splitting purpose, it would be nice to be able to select one of them.
  2. The documentation says "with background features in gray", but what exactly are these gray dots? When I select different clusters, the gray dots also seem to change, suggesting that they are not randomly chosen.
  3. When the black dots are intermingled with gray ones, it appears that the isolation of the select cluster is not great. Is this generally the case?

I understand the you left JRClust project already, but the documentation only shows the definition of each window for manual curation. It does not tell us how the manual curation goes typically. It would be nice to have step by step walk through, because I found it hard to understand what to see in what order.

For example, I'd suggest something like below using the sample data provided.

  1. Focus on Averaged waveform window first. Move to the leftmost clusters by dragging.
  2. Click the cluster 1 in the window. Check if .....
  3. Then click the cluster 3. The feature-vs-time view shows spikes in the cluster are intermingled with gray dots, i.e. background, so the isolation is poor. Choose Unit 3 > noise or type d to delete the cluster.
  4. etc...

Also I'd like to see the good example of a result of manual curation phase using the sample data. At the end how many single units did you find in the sample data (128 channels for 5 min?), for instance? How long the manual curaton may take?

Best regards, Kouichi

kouichi-c-nakamura commented 4 years ago

The features shown for the selected cluster are in black, with background features in gray (toggle background features with the b key)

At least I figured out that "background features" (gray) means the features (eg. Vpp = the amplitude between negative peak to positive peak) of the other clusters than the selected cluster (black) recorded in the same site (in the example below, Site 13 as shown on the left). They are shown in "The waveform view" horizontally in the same row (eg. Site 13).

figtime

So when black dots (selected cluster) are intermingled with gray ones, that means that the selected clusters are not different from the other clusters found in the same site in terms of the features (eg. Vpp).

Still not sure what the red rectangle is for.