Comments (4)
Hi Simon,
Thank you for question and I am glad you're enjoying bombcell!
Bombcell stores the unit ID for each unit in qMetric.clusterID
, this corresponds to the kilosort/phy label + 1 (the +1 makes it 1-indexed, and easier to use in MATLAB). I've just pushed a change so it's clearer by adding a field qMetric.phy_clusterID
that directly gives you the kilosort/phy label.
The value in qMetric.clusterID
value does not necessarily correspond to the row in the qMetric
structure the unit is in (ie for unit say 5, it might be in row 3 for instance), because kilosort drops units in the last stages of the algorithm but does not rename them, leading to some empty units.
I pushed changes yesterday to make this clearer. There's now a little blurb and example at the end of bc_qualityMetrics_pipeline
, and the GUI now displays all three values: the clusterID, the phy clusterID and the row the unit is in (see image below for what it should look like now)
from bombcell.
To answer you question about spikes, spike times per unit are extracted with the function bc_loadEphysData
. If you use the bc_qualityMetrics_pipeline
script, they will be stored in spikeTimes_samples
. To get them into seconds, divide spikeTimes_samples
by your ephys sampling rate (usually 30000 samples/second).
from bombcell.
Thanks for the answers! It is clear now.
from bombcell.
Great! Closing the issue now. Don't hesitate to open it back up or create a new one if you have any other questions or issues.
from bombcell.
Related Issues (20)
- another small bug HOT 1
- Unrecognized function or variable 'Vrange' error while running pipeline HOT 2
- unitType in Phy HOT 2
- 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
- Error in plotting quality metrics of data sorted with kilosort4 HOT 4
- Issue extracting quality metrics for data spike sorted using Kilosort4 HOT 3
- fontname function introduced after R2022b HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bombcell.