Comments (4)
Hi Julie, this works perfectly! Thank you so much,
Johanna
from bombcell.
Hi Johanna,
Thanks for your message! Bombcell hasn't been fully tested with Kilosort4 yet. Would you be able to send me your qMetric
and param
structures that bombcell computes (the inputs to bc_plotGlobalQualityMetric
) so I can troubleshoot?
from bombcell.
Hi Julie, sure. Here are the files:
param_Johanna.csv
qMetric_Johanna.csv
from bombcell.
Hi Johanna,
Thank you very much!
I had a quick look at the error was because in this dataset no units were being classified as Good or MUA (so there was nothing to plot on the second upSet plot, and that caused on error) - you can see in the first upSet plot (below)
. This is now fixed - bombcell will display a text warning you there are no units in a catagery but won't error anymore.
This classification was due to most of your units being classified as noise with a waveform baseline flatness
above the threshold, and this is because Kilosort4 extracts templates differently than previous Kilosort versions. It used to be 82 samples and it is now 61, which means the baseline window we define with param.waveformBaselineWindowStart
, param.waveformBaselineWindowStop
awas now wrong, and usually included the units' main trough/peak. I have now added an input kilosortVersion
in bc_qualityParamValues
to get values that make more sense for kilosort4.
Let me know if this works better for you!
from bombcell.
Related Issues (20)
- how to make a .oebin file for multiple day recordings and after cutting bad channels HOT 1
- classification in somatic and non-somatic units HOT 3
- bug report HOT 2
- issue with computation of timeChunks HOT 1
- classification of MUA HOT 1
- error with bc_loadMetricsForGUI HOT 7
- mismatch between qcMetrics rows and number of units
- tauC value HOT 3
- Error in bc_waveformShape HOT 11
- Bug Report HOT 2
- fontname in prettify_plot.m requires one more input HOT 1
- bc_classifyCells needs `region` as third input argument HOT 1
- max drift.tsv has NaN values HOT 3
- Depth relative to probe tip? HOT 1
- Issue extracting quality metrics for data spike sorted using Kilosort4 HOT 3
- fontname function introduced after R2022b HOT 3
- Discrepancy between ContamPct and frac_RPVs HOT 7
- Question with bc_getDistanceMetrics HOT 4
- Maximum waveform channel different between templates and the average extracted waveform. HOT 1
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from bombcell.