Kilosort v4.0.18

This release adds a fix for warnings related to conflicting BLAS and OpenMP implementations, as well as other misc bug fixes. It also adds logging for resource usage throughout the sorting pipeline.

Full Changelog: v4.0.15...v4.0.18

Kilosort v4.0.15

This release adds:

• Option to specify channels to exclude from sorting through the API and GUI.
• Documentation for output files.
• A new tutorial notebook demonstrating how to modify good/mua labels using custom criteria.
• Option to force-clear PyTorch's reserved GPU memory between some operations, using clear_cache = True.

Full Changelog: v4.0.14...v4.0.15

v4.0.13

This release contains several bug fixes, changes the duplicate_spike_bins parameter to duplicate_spike_ms (new default 0.25), adds the highpass_cutoff parameter, and improves logging of error messages.

Full Changelog: v4.0.12...v4.0.13

Kilosort v4.0.12

This release adds the option to save a drift-corrected copy of the data to temp_wh.dat in the results directory. This can be done through the API using save_preprocessed_copy=True for run_kilosort, or by clicking the checkbox with the same name under the "Run" button in the GUI. Using either option will also update options for Phy so that this copy of the data is used instead of the raw data.

Full Changelog: v4.0.11...v4.0.12

v4.0.11

In addition to some minor fixes and additions to logging behavior, this release addresses the following problems:

• Negative spike times will no longer be detected.
• Plots generated by GUI will be saved in the results directory in .png format.
• .mat probe files will correctly load kcoords (shank index) for probes with disconnected channels.
• template placement is handled separately for each shank, so that the spacing between shanks will not affect template positions.
• added new shift and scale parameters for handling float32 data better.

Full Changelog: v4.0.8...v4.0.11

Kilosort v4.0.8

This release adds a new parameter, drift_smoothing, which controls the amount of gaussian smoothing applied to the spatiotemporal drift estimation. It also switches control of console output to the logging module and adds a kilosort.log file to the sorting results.

Full Changelog: v4.0.7...v4.0.8

Kilosort v4.0.7

This release adjusts saved template amplitudes, which fixes a template scaling issue in Phy and affects the displayed amplitude values for Phy. It also reverts a "fix" that was added to stop negative spike times from showing up for the first data batch, since that was causing a misalignment issue. Negative spike times are currently possible again, but should be rare - a message will show up after the spike detection step if any negative spike times are found, until we figure out what's causing this.

Full Changelog: v4.0.6...v4.0.7

Kilosort v4.0.6

Along with miscellaneous bug fixes, this release allows some sections of the GUI to be resized. After installing, you will probably notice that the proportions have changed. You can customize this yourself by clicking and dragging on the handles shown in the image below (circled red). Any resizing will be saved and restored the next time you open the GUI.

Full Changelog: v4.0.4...v4.0.6

Kilosort 2 patch1

This release fixes a bug for the spike holes problem (issue #594). The default value of the NT parameter has changed to 65,472 in configFile384. You need to use these defaults to fix the spike holes problem (or the rules specified in configFile384 for NT and ntbuff). Please recompile the CUDA functions with mexGPUall.

The release will be updated if further modifications are made (patch2, 3 etc).

Note: this aligns the changes in Kilosort 2.0.2 to those in 2.5.2 and 3.0.2.

Kilosort v4.0.4

Sorting should now work for multi-shank probes without needing to vertically stack the shanks.

This release adds distance gating for universal template positions, to match the behavior of previous versions of Kilosort. By default, templates will be excluded if they are farther than max(dmin, dminx) microns from the nearest active site. This can be adjusted manually by changing the new max_channel_distance parameter in "Extra settings." Universal template placement can be previewed in the GUI by checking "Universal Templates" under the probe plot. Note that changing any of dmin, dminx or max_channel_distance will change the positions of the universal templates, but this will not show on the plot until you change one of the other options or click "Preview Probe" again. The probe plot also includes axes to show scale, and a "True Aspect Ratio" checkbox to switch to a physically proportional representation.

Additionally, center points for template groupings are now determined in a way that should work well for multi-shank probes, removing the need for artificially stacking shanks on top of one another. The placement of these grouping centers can also be previewed in the GUI by checking "Grouping Centers" under the probe plot. You should see one column of centers on each shank. If this is not happening, or if you're using a 2D array, you may need to specify the new x_centers parameter in "Extra settings."

Full Changelog: v4.0.3...v4.0.4