Skip to content

Commit

Permalink
Added note about kcoords to docs
Browse files Browse the repository at this point in the history
  • Loading branch information
jacobpennington committed Jun 27, 2024
1 parent 2e7547c commit 3e010bb
Show file tree
Hide file tree
Showing 2 changed files with 3 additions and 1 deletion.
2 changes: 1 addition & 1 deletion docs/gui_guide.rst
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ To select a probe, click the drop-down menu just below "Select Probe Layout." Th
.. image:: https://www.kilosort.org/static/images/gui_select_probe.png
:width: 600

If you need to create a new probe layout, select "[new]" to open the probe creation tool. Values for 'x-coordinates' and 'y-coordinates' need to be in microns, and can be specified with numpy expressions. For example, a 1-shank linear probe with 4 channels could have `np.ones(4)` in the 'x-coordinates' field instead of `1, 1, 1, 1`. Each field (except name) must have the same number of elements, corresponding to the number of ephys channels in the data. WHen you are finished setting the values, click "Check" to verify that your inputs are valid. If they are not, an error message will be displayed. Otherwise, the "OK" button will become clickable, which will save the probe to the Kilosort4 probes directory.
If you need to create a new probe layout, select "[new]" to open the probe creation tool. Values for 'x-coordinates' and 'y-coordinates' need to be in microns, and can be specified with numpy expressions. For example, a 1-shank linear probe with 4 channels could have `np.ones(4)` in the 'x-coordinates' field instead of `1, 1, 1, 1`. Each field (except name) must have the same number of elements, corresponding to the number of ephys channels in the data. When you are finished setting the values, click "Check" to verify that your inputs are valid. If they are not, an error message will be displayed. Otherwise, the "OK" button will become clickable, which will save the probe to the Kilosort4 probes directory.

.. image:: https://www.kilosort.org/static/images/gui_make_probe.png
:width: 600
Expand Down
2 changes: 2 additions & 0 deletions docs/parameters.rst
Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,8 @@ This is the number of time samples used to represent spike waveforms, as well as
----------------------
These adjust the vertical and lateral spacing, respectively, of the universal templates used during spike detection, as well as the vertical and lateral sizes of channel neighborhoods used for clustering. By default, Kilosort will attempt to determine a good value for ``dmin`` based on the median distance between contacts, which tends to work well for Neuropixels-like probes. However, if contacts are irregularly spaced, you may need to specify this manually. The default for ``dminx`` is 32um, which is also well suited to Neuropixels probes. For other probes, try setting ``dminx`` to the median lateral distance between contacts as a starting point.

Note that as of version 4.0.11, the ``kcoords`` variable in the probe layout will be used to restrict template placement within each shank. Each shank should have a unique ``kcoords`` value that is the same for all contacts on that shank.

``min_template_size``
---------------------
This sets the standard deviation of the smallest Gaussian spatial envelope used to generate universal templates, with a default of 10 microns. You may need to increase this for probes with wider spaces between contacts.
Expand Down

0 comments on commit 3e010bb

Please sign in to comment.