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marius10p committed Nov 14, 2020
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Expand Up @@ -10,7 +10,7 @@ Kilosort2.5 improves on Kilosort2 primarily in the type of drift correction we u

Kilosort2 can still be accessed by downloading the release "Kilosort 2.0". It improves on the original Kilosort primarily by employing drift correction, which changes the templates continuously as a function of drift. Drift correction does not depend on a particular probe geometry, but denser spacing of sites generally helps to better track neurons, especially if the probe movement is large. Kilosort2 has been primarily developed on awake, head-fixed recordings from Neuropixels 1.0 data, but has also been tested in a few other configurations. To get a sense of how probe drift affects spike sorting, check out our "eMouse" simulation [here](https://github.com/MouseLand/Kilosort2/tree/master/eMouse_drift) and [its wiki page](https://github.com/MouseLand/Kilosort2/wiki/4.-eMouse-simulator-with-drift).

To aid in setting up a Kilosort2/2.5 run on your own probe configuration, we have developed a [graphical user interface](https://github.com/MouseLand/Kilosort2/wiki/1.-The-GUI) where filepaths can be set and data loaded and visually inspected, to make sure Kilosort2.5 sees it correctly. The picture above is another GUI visualization: it shows the templates detected by Kilosort2.5 over a 60ms interval from a Neuropixels recording. The final output of Kilosort2 can be visualized and curated in the [Phy GUI](https://github.com/kwikteam/phy), which must be installed separately (we recommend the development version). Since Phy is in Python, you will also need the [npy-matlab ](https://github.com/kwikteam/npy-matlab) package.
To aid in setting up a Kilosort2/2.5 run on your own probe configuration, we have developed a [graphical user interface](https://github.com/MouseLand/Kilosort/wiki/1.-The-GUI) where filepaths can be set and data loaded and visually inspected, to make sure Kilosort2/2.5 sees it correctly. The picture above is another GUI visualization: it shows the templates detected by Kilosort2 over a 60ms interval from a Neuropixels recording. The final output of Kilosort2/2.5 can be visualized and curated in the [Phy GUI](https://github.com/kwikteam/phy), which must be installed separately. Since Phy is in Python, you will also need the [npy-matlab ](https://github.com/kwikteam/npy-matlab) package.

### Installation ###

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