Cluster view and Similarity View blank

[Coglet00]

i was trouble shooting this problem because both views are blank even when env QTWEBENGINE_CHROMIUM_FLAGS="--single-process is used before opening phy. This had worked for many others. i heard about the readCSVfunction (https://github.com/cortex-lab/spikes/blob/master/preprocessing/phyHelpers/readClusterGroupsCSV.m) as this might be useful for reading cluster_group.tsv file.

i am a bit inexperienced so i dont know how to exactly integrate this new fucntion in matlab. like in what folder do i put it and where do i call it?

thanks for help!

[zm711]

@Coglet00,

Could you post any errors your getting here. This can be done by running fine in debug mode like this:

phy template-gui path/to/parms.py --debug

Then copy the log info. I'm not quite sure what you're actually asking at the moment. the spikes repo that you are mentioning is for post processing of phy data not for use inside of Phy. But maybe you're asking a couple different things?

[ashsrobbins]

@zm711 I have the same issue on Ubuntu right now:

Here is the log when I click on a cluster (I can click them, just not see them).

14:51:30.695 [D] init:68 Start capturing exceptions. 14:51:30.696 [W] model:1408 File traces_cached_seg0.raw does not exist. 14:51:30.741 [W] model:603 Unreferenced clusters found in templates (generally not a problem) 14:51:30.771 [D] model:619 Loading spike clusters. 14:51:30.803 [W] model:625 Unreferenced clusters found in spike_clusters (generally not a problem) 14:51:30.835 [D] model:569 No channel shank file found. 14:51:30.836 [D] model:692 Loading templates. 14:51:30.856 [D] model:724 Templates are dense. 14:51:30.857 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed. 14:51:30.857 [D] model:730 Loading the whitening matrix. 14:51:30.861 [D] model:737 Loading the inverse of the whitening matrix. 14:51:30.866 [W] traces:462 File /media/danser-lab/hippo1/cartpole/24-01-07_data/20217/exp1/results_KS2_stitch/sorter_output/traces_cached_seg0.raw does not exist. 14:51:30.866 [W] traces:462 File /media/danser-lab/hippo1/cartpole/24-01-07_data/20217/exp1/results_KS2_stitch/sorter_output/traces_cached_seg0.raw does not exist. 14:51:30.866 [D] model:766 Loading features. 14:51:30.866 [D] model:781 Features are sparse. 14:51:30.867 [D] model:803 Loading template features. 14:51:30.867 [D] model:813 Template features are sparse. 14:51:30.867 [D] model:504 Load cluster_KSLabel.tsv. 14:51:30.868 [D] model:504 Load cluster_ContamPct.tsv. 14:51:30.869 [D] model:504 Load cluster_Amplitude.tsv. 14:51:30.870 [D] model:504 Load cluster_group.tsv. 14:51:31.036 [D] context:100 Initialize joblib cache dir at /media/danser-lab/hippo1/cartpole/24-01-07_data/20217/exp1/results_KS2_stitch/sorter_output/.phy. 14:51:31.037 [D] context:101 Reducing the size of the cache if needed. 14:51:31.043 [D] base:102 Add filter high_pass. 14:51:31.043 [D] config:31 Load config file /home/danser-lab/.phy/phy_config.py. 14:51:31.043 [D] plugin:145 Loading 0 plugins. 14:51:31.043 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms. 14:51:31.044 [D] context:126 Load memcache for phy.apps.base._get_mean_waveforms. 14:51:31.044 [D] context:126 Load memcache for phy.apps.base._get_template_waveforms. 14:51:31.044 [D] context:126 Load memcache for phy.apps.base.get_mean_spike_template_amplitudes. 14:51:31.044 [D] context:126 Load memcache for phy.apps.base.get_template_counts. 14:51:31.044 [D] context:126 Load memcache for phy.apps.base.get_template_for_cluster. 14:51:31.045 [D] context:126 Load memcache for phy.apps.template.gui.get_template_amplitude. 14:51:31.046 [D] context:126 Load memcache for phy.apps.base.get_cluster_amplitude. 14:51:31.046 [D] context:126 Load memcache for phy.apps.base.get_mean_firing_rate. 14:51:31.046 [D] context:126 Load memcache for phy.apps.base.get_best_channel. 14:51:31.046 [D] context:126 Load memcache for phy.apps.template.gui.get_best_channels. 14:51:31.047 [D] context:126 Load memcache for phy.apps.base.get_channel_shank. 14:51:31.047 [D] context:126 Load memcache for phy.apps.base.get_probe_depth. 14:51:31.047 [D] context:126 Load memcache for phy.apps.base.peak_channel_similarity. 14:51:31.073 [D] context:185 Save data to /media/danser-lab/hippo1/cartpole/24-01-07_data/20217/exp1/results_KS2_stitch/sorter_output/.phy/spikes_per_cluster.pkl. 14:51:31.131 [D] gui:463 Creating GUI. 14:51:31.136 [D] state:46 Load /home/danser-lab/.phy/TemplateGUI/state.json for GUIState. 14:51:31.136 [D] state:46 Load /media/danser-lab/hippo1/cartpole/24-01-07_data/20217/exp1/results_KS2_stitch/sorter_output/.phy/state.json for GUIState. 14:51:31.265 [D] gui:718 Add view ClusterView to GUI. 14:51:31.275 [D] gui:718 Add view SimilarityView to GUI. 14:51:31.306 [D] gui:718 Add view WaveformView to GUI. 14:51:31.309 [D] base:337 Set state for WaveformView. 14:51:31.319 [D] gui:718 Add view CorrelogramView to GUI. 14:51:31.321 [D] base:337 Set state for CorrelogramView. 14:51:31.340 [D] gui:718 Add view ISIView to GUI. 14:51:31.341 [D] base:337 Set state for ISIView. 14:51:31.352 [D] gui:718 Add view FeatureView to GUI. 14:51:31.354 [D] base:337 Set state for FeatureView. 14:51:31.372 [D] gui:718 Add view AmplitudeView to GUI. 14:51:31.373 [D] base:337 Set state for AmplitudeView. 14:51:31.391 [D] gui:718 Add view FiringRateView to GUI. 14:51:31.393 [D] base:337 Set state for FiringRateView. 14:51:31.659 [D] gui:718 Add view ProbeView to GUI. 14:51:31.661 [D] base:337 Set state for ProbeView. 14:51:31.676 [D] gui:718 Add view ClusterScatterView to GUI. 14:51:31.678 [D] base:337 Set state for ClusterScatterView. 14:51:31.678 [D] base:494 Set color scheme to random. 14:51:31.679 [D] base:1626 Adding default color schemes to ClusterScatterView. 14:51:31.714 [D] gui:718 Add view ClusterScatterView to GUI. 14:51:31.715 [D] base:337 Set state for ClusterScatterView (1). 14:51:31.715 [D] base:494 Set color scheme to random. 14:51:31.716 [D] base:1626 Adding default color schemes to ClusterScatterView (1). 14:51:31.758 [D] gui:519 Load the geometry state. 14:51:32.268 [D] supervisor:817 Clusters selected: [30] (36) 14:53:22.026 [D] supervisor:817 Clusters selected: [22] (37) 14:53:23.821 [D] supervisor:839 Similar clusters selected: [178] (164) 14:53:25.309 [D] supervisor:817 Clusters selected: [294] (170)

[zm711]

Hi @ashsrobbins,

Looks like you're probably doing this through spikeinterface? Could you post what inside the params.py file (it should have the raw/dat file path, n_channels, etc.

[ashsrobbins]

Hey @zm711!

Yes spikeinterface and kilosort2.

params.py:

n_channels_dat = 951
dtype = 'int16'
offset = 0
sample_rate = 20000.
hp_filtered = False

[zm711]

Is there no dat_path given? (or did you delete it for privacy). We really should have spikeinterface indicate where the .dat is.

[ashsrobbins]

Ahh, apologies, I accidentally removed it:

dat_path = 'traces_cached_seg0.raw'
n_channels_dat = 951
dtype = 'int16'
offset = 0
sample_rate = 20000.
hp_filtered = False

I'll check with some of my old recordings, because I have opened phy before successfully with data sorted in this same way. However I just recently created a new conda env and followed the install directions on the main page, causing this error.

[zm711]

There are some bugs with the main page install. We can try something to fix it:

Instead could you download the environment.yaml from the root directory in this repo. Then open it and edit for python<3.12 (there's an issue with 3.12 just waiting for my PR to be merged to fix it). Then recreate the environment that way by creating the environment with a file.

[zm711]

With python 3.11 which is now enforced by the yaml this should be fixed.