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25 results for “spikeinterface”
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Please join us at the next session of the INCF/OCNS Software WG: Pierre Yger will present #SpikeInterface: 14 May 2024 at 1500 UTC. More info:
https://ocns.github.io/SoftwareWG/2024/05/07/wg-meeting-14-may-2024-spikeinterface-pierre-yger-.html
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#ephys and #spikesorting community!We are thrilled to announce the "Tools and Methods for Next Generation Electrophysiology" event, happening in Edinburgh from May 27-31.
Registration link:
https://forms.gle/6dEdeR7sD7u6u8rU8More info on the event webpage:
https://spikeinterface.github.io/spikeinterface-events/spikeinterface-workshop-2024/ -
#NeuroMastodon #ephys #spikesorting
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SpikeInterface v0.99.0 has been released on #PyPi!https://pypi.org/project/spikeinterface/0.99.0/
Just run this to upgrade your installation:
>>> pip install --upgrade spikeinterface
Check out the release notes here:
https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html -
#NeuroMastodon #ephys #spikesorting
SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/
Just run:
>>> pip install --upgrade spikeinterfaceThe new release includes several new features and updates to the package! A detailed list of changes can be found here:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.htmlHappy #spikesorting to everyone!!!
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#spikesorting #electrophysiology
Happy new year from the SpikeInterface team! 🥳
2023 will be full of updates and new exciting features!If you'd like to support us and broaden the SI community, please add a ⭐️ to our GitHub page 🙏:
https://github.com/SpikeInterface/spikeinterface -
SpikeInterface is an #opensource framework in #python to analyze extracellular electrophysiology #ephys data and perform #spikesorting.
We believe that spike sorting development should be a collaborative and community effort and we encourage contributors!
You can read more in the docs:
https://spikeinterface.readthedocs.io/en/latest/Follow a tutorial:
https://github.com/SpikeInterface/spiketutorialsCheck out the source code:
https://github.com/SpikeInterface/spikeinterface/Happy #spikesorting to all!
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#NeuroMastodon #ephys #spikesorting
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SpikeInterface v0.99.0 has been released on #PyPi!https://pypi.org/project/spikeinterface/0.99.0/
Just run this to upgrade your installation:
>>> pip install --upgrade spikeinterface
Check out the release notes here:
https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html -
#NeuroMastodon #ephys #spikesorting
📢📢📢📢📢
SpikeInterface v0.99.0 has been released on #PyPi!https://pypi.org/project/spikeinterface/0.99.0/
Just run this to upgrade your installation:
>>> pip install --upgrade spikeinterface
Check out the release notes here:
https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html -
#NeuroMastodon #ephys #spikesorting
📢📢📢📢📢
SpikeInterface v0.99.0 has been released on #PyPi!https://pypi.org/project/spikeinterface/0.99.0/
Just run this to upgrade your installation:
>>> pip install --upgrade spikeinterface
Check out the release notes here:
https://spikeinterface.readthedocs.io/en/0.99.0/releases/0.99.0.html -
#NeuroMastodon #ephys #spikesorting
SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/
Just run:
>>> pip install --upgrade spikeinterfaceThe new release includes several new features and updates to the package! A detailed list of changes can be found here:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.htmlHappy #spikesorting to everyone!!!
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#NeuroMastodon #ephys #spikesorting
SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/
Just run:
>>> pip install --upgrade spikeinterfaceThe new release includes several new features and updates to the package! A detailed list of changes can be found here:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.htmlHappy #spikesorting to everyone!!!
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#NeuroMastodon #ephys #spikesorting
SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/
Just run:
>>> pip install --upgrade spikeinterfaceThe new release includes several new features and updates to the package! A detailed list of changes can be found here:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.htmlHappy #spikesorting to everyone!!!
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#NeuroMastodon #ephys #spikesorting
SpikeInterface v0.97.0 has been released on #PyPi: https://pypi.org/project/spikeinterface/
Just run:
>>> pip install --upgrade spikeinterfaceThe new release includes several new features and updates to the package! A detailed list of changes can be found here:
https://spikeinterface.readthedocs.io/en/latest/releases/0.97.0.htmlHappy #spikesorting to everyone!!!
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Are you interested in the spiking activity of your neuronal cultures, #brain slices, #organoids, etc.?
Check out our latest publication in STAR Protocols:
“Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst”
https://doi.org/10.1016/j.xpro.2025.104195It provides user-friendly graphical and #Python programming interfaces to spike sorting via template matching thanks to #Kilosort and #spikeinterface (@spikeinterface), and subsequent analysis of #spiking and #bursting activity, networks, and synchrony.
#neuroscience #brainscience #electrophysiology #brainOrganoids
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Spent a month in procrastination to avoid debugging a horribly patched #spikesorting pipeline in MATLAB. Then came to discover @spikeinterface and now I just want to spend my day plotting filtered traces and quality metrics, everything is just so smooth 😍
People in #open neuroscience software are pulling out truly amazing things! -
#SpikeSorting question:
Say I would like to use #Klustakwick (3) - I have the .exe of it - with #SpikeInterface , to pre-sort my spikes. But it is not implemented in the available “sorters”.
“Klusta” is, which seems somewhat similar (made by the same people?) but also quite different. I really like Klustakwick and would just like to try that.
Any ideas?
Where is the best place to ask questions about SpikeInterface? I feel like opening an Issue on the GitHub is a bit overkill… 🙏 -
Hi, is anyone using #Mountainsort with #Neuralynx data? Are you using #SpikeInterface to convert the input data? Would you share your code? 😃🙏
#SpikeSorting -
@chrisXrodgers
Very good question!
I have most recently used MountainSort + Phy (via SpikeInterface) and I quite like Phy (for manual refinement of clusters) but not so much Mountainsort - it seemed very conservative. I’ll go back to it soon and tweak the settings a bit. If you want to try it out we have some shared code with the Genzel lab here: https://github.com/elduvelle/SpikeinterfaceMS4_GenzelLabBut I was also going to try out Kilosort. Do you really not like it?
Before that KlustaKwik + Tint has been the gold standard for me :) … but maybe it’s time to move on!
#SpikeSorting #Tetrodes #Electrophysiology -
What is #neuronalSpiking? Neurons in the brain use electrical signals to communicate with each other and with the body. Each time a neuron is electrically active and this activity exceeds some threshold we can detect this activity as a spike.
Here, we used high-dimensional multielectrode arrays (HD-MEA) with thousands of electrodes, able to measure extracellular electrical potentials of single neurons. The recorded data consisted of raw voltage traces sampled at low frequency of 20 kHz for each of thr 4,096 recording channels. We implemented the reading of these data in #spikeinterface and could reuse the spikeinterface methods to run the spike detection and sorting with #Kilosort.
#SpikeSorting is important because, firstly, neuronal units may span over multiple electrodes, and secondly, an electrode may measure activity from multiple nearby neuronal units. To study biological questions it was essential to measure the spiking activity of real neuronal units instead of electrodes.
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What is #neuronalSpiking? Neurons in the brain use electrical signals to communicate with each other and with the body. Each time a neuron is electrically active and this activity exceeds some threshold we can detect this activity as a spike.
Here, we used high-dimensional multielectrode arrays (HD-MEA) with thousands of electrodes, able to measure extracellular electrical potentials of single neurons. The recorded data consisted of raw voltage traces sampled at low frequency of 20 kHz for each of thr 4,096 recording channels. We implemented the reading of these data in #spikeinterface and could reuse the spikeinterface methods to run the spike detection and sorting with #Kilosort.
#SpikeSorting is important because, firstly, neuronal units may span over multiple electrodes, and secondly, an electrode may measure activity from multiple nearby neuronal units. To study biological questions it was essential to measure the spiking activity of real neuronal units instead of electrodes.
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What is #neuronalSpiking? Neurons in the brain use electrical signals to communicate with each other and with the body. Each time a neuron is electrically active and this activity exceeds some threshold we can detect this activity as a spike.
Here, we used high-dimensional multielectrode arrays (HD-MEA) with thousands of electrodes, able to measure extracellular electrical potentials of single neurons. The recorded data consisted of raw voltage traces sampled at low frequency of 20 kHz for each of thr 4,096 recording channels. We implemented the reading of these data in #spikeinterface and could reuse the spikeinterface methods to run the spike detection and sorting with #Kilosort.
#SpikeSorting is important because, firstly, neuronal units may span over multiple electrodes, and secondly, an electrode may measure activity from multiple nearby neuronal units. To study biological questions it was essential to measure the spiking activity of real neuronal units instead of electrodes.
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Are you interested in the spiking activity of your neuronal cultures, #brain slices, #organoids, etc.?
Check out our latest publication in STAR Protocols:
“Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst”
https://doi.org/10.1016/j.xpro.2025.104195It provides user-friendly graphical and #Python programming interfaces to spike sorting via template matching thanks to #Kilosort and #spikeinterface (@spikeinterface), and subsequent analysis of #spiking and #bursting activity, networks, and synchrony.
#neuroscience #brainscience #electrophysiology #brainOrganoids
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Are you interested in the spiking activity of your neuronal cultures, #brain slices, #organoids, etc.?
Check out our latest publication in STAR Protocols:
“Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst”
https://doi.org/10.1016/j.xpro.2025.104195It provides user-friendly graphical and #Python programming interfaces to spike sorting via template matching thanks to #Kilosort and #spikeinterface (@spikeinterface), and subsequent analysis of #spiking and #bursting activity, networks, and synchrony.
#neuroscience #brainscience #electrophysiology #brainOrganoids
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Are you interested in the spiking activity of your neuronal cultures, #brain slices, #organoids, etc.?
Check out our latest publication in STAR Protocols:
“Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst”
https://doi.org/10.1016/j.xpro.2025.104195It provides user-friendly graphical and #Python programming interfaces to spike sorting via template matching thanks to #Kilosort and #spikeinterface (@spikeinterface), and subsequent analysis of #spiking and #bursting activity, networks, and synchrony.
#neuroscience #brainscience #electrophysiology #brainOrganoids
-
Are you interested in the spiking activity of your neuronal cultures, #brain slices, #organoids, etc.?
Check out our latest publication in STAR Protocols:
“Protocol for the enhanced analysis of electrophysiological data from high-density multi-electrode arrays with nicespike and spikeNburst”
https://doi.org/10.1016/j.xpro.2025.104195It provides user-friendly graphical and #Python programming interfaces to spike sorting via template matching thanks to #Kilosort and #spikeinterface (@spikeinterface), and subsequent analysis of #spiking and #bursting activity, networks, and synchrony.
#neuroscience #brainscience #electrophysiology #brainOrganoids