diff --git a/README.md b/README.md index 401d8472..0ecd1ffa 100644 --- a/README.md +++ b/README.md @@ -24,9 +24,7 @@ Example notebooks are provided in the `docs/source/tutorials` folder and in the **If you use Kilosort1-4, please cite the [paper](https://www.nature.com/articles/s41592-024-02232-7):** Pachitariu, M., Sridhar, S., Pennington, J., & Stringer, C. (2024). Spike sorting with Kilosort4. -**Note on multi-shank probes** : We are aware of some issues with sorting data from probes with multiple shanks or 2D arrays. See [documentation here](https://kilosort.readthedocs.io/en/latest/multi_shank.html) for recommended workarounds until the code is updated to handle these probes. - -**Note on reusing parameters from previous versions**: This probably will not work well. Kilosort4 is a new algorithm, and the main parameters (the thresholds) can affect the results in a different way for your data. Please start with the default parameters and adjust from there based on what you see in Phy. +**Note on reusing parameters from previous versions**: This probably will not work well. Kilosort4 is a new algorithm, and the main parameters (the thresholds) can affect the results in a different way for your data. Please start with the default parameters and adjust from there based on what you see in Phy. For descriptions of Kilosort4's parameters, you can mouse-over their names in the GUI or look at `kilosort.parameters.py`. **Warning** :bangbang:: There were two bugs in Kilosort 2, 2.5 and 3 (but not 4) which caused fewer spikes to be detected in ~7ms periods at batch boundaries (every 2.1866s, issue #594). The patch1 releases fix these bugs, please use the new default NT and ntbuff parameters. diff --git a/docs/index.rst b/docs/index.rst index af8248f8..d4f69988 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -14,7 +14,6 @@ please see our pre-print on `BioArxiv gui_guide parameters - multi_shank hardware drift diff --git a/docs/multi_shank.rst b/docs/multi_shank.rst deleted file mode 100644 index 9d030019..00000000 --- a/docs/multi_shank.rst +++ /dev/null @@ -1,11 +0,0 @@ -.. _multi_shank: - -Using probes with multiple shanks -================================== -Update: the latest version of the code addresses this issue. After getting feedback from users, this page will be removed if there are no further issues. For 2D arrays, you may want to set the new `x_centers` parameter (under "Extra Settings" in the GUI) for best results. - -Currently, Kilosort4 does not process shanks separately. Until this is added, we recommend changing your probe layout to artificially stack the shanks in a single column with a bit of vertical space (~100um) between each shank. - -If that option isn't feasible for some reason, you can also try adjusting the `min_template_size` and/or `dminx` parameters in the GUI, or in the settings argument for `run_kilosort` if you're using the API. Setting `dminx` to around half the total width of the probe seems to be a good starting point, and you can adjust from there. - -See `issue 606 `_ and `issue 617 `_ for additional context. \ No newline at end of file