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flatironinstitute / qt-mountainview

Visualization of spike sorting experiments to be used as a plugin package to mountainlab-js
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qt-mountainview visualization troubles #10

Open MarcoUniPr opened 5 years ago

MarcoUniPr commented 5 years ago

Dear all, my lab used an older version of mountainsort and thus of mountainlab and it worked perfectly. Just now I installed the new version of mountainlab-js, mountainsort as well as qt-mountainview through CONDA. I tried to make a sorting of my own 16 channels and it looks working good. Unfortunaly, when I try to visualize cluster metrics I am not able to see them. I can visualize "Detail", cross-correlograms, and several other issues, but I cannot se cluster metrics which is fundamental for me to establish if a waveform is a single unit or a multiunit. Moreover, if one try to open the settings icon in upper right part of the Detail panel, I cannot select anything. How can I solve this problems? Can you help me? Thanks in advance best Marco

tjd2002 commented 5 years ago

Are there any messages printed on the console (i.e. the command line prompt where you launch qt-mountainview) when you try to view cluster metrics?

tjd2002 commented 5 years ago

Also, can you paste in the commands you are using to launch qt-mountainview? You need to tell qt-mountainview where your metrics file is located with: --cluster_metrics=/path/to/cluster_metrics.json

MarcoUniPr commented 5 years ago

Ok. In order to sort my own data I run the following code (i.e. ms4_sort_bash.sh):

!/bin/bash

set -e

mkdir -p output

Preprocess

ml-run-process ephys.bandpass_filter \ --inputs timeseries:DATASET/dataset4/SAND_AIP_15-06-2016_Merged_CH017_CH032.mda \ --outputs timeseries_out:output/filt.mda.prv \ --parameters samplerate:30000 freq_min:300 freq_max:6000 ml-run-process ephys.whiten \ --inputs timeseries:output/filt.mda.prv \ --outputs timeseries_out:output/pre.mda.prv

Spike sorting

ml-run-process ms4alg.sort \ --inputs \ timeseries:output/pre.mda.prv geom:DATASET/dataset4/geom.csv \ --outputs \ firings_out:output/firings.mda \ --parameters \ detect_sign:-1 \ adjacency_radius:1 \ detect_threshold:3

Compute templates

ml-run-process ephys.compute_templates \ --inputs timeseries:DATASET/dataset4/SAND_AIP_15-06-2016_Merged_CH017_CH032.mda firings:output/firings.mda \ --outputs templates_out:output/templates.mda.prv \ --parameters \ clip_size:150

%%%%%% Once I sorted data, I run the following command:

qt-mountainview --raw DATASET/dataset4/SAND_AIP_15-06-2016_Merged_CH017_CH032.mda --filt output/filt.mda.prv --pre output/pre.mda.prv --samplerate 30000 --firings output/firings.mda