v3.2.4

Bugfix: Manual GUI: projection display is correctly updated.
Previously the second unit selection (shown in red) required two right clicks to update.

v3.2.3

1. Bugfix: incorrect "gather" function was called when Bigdata toolbox is installed in Matlab R2017.

2. Faster and more robust fft_clean operation (run if fft_thresh > 0)
   It can handle a limited GPU memory.
   nLoads_gpu parameter is introduced, which is the ratio of the system memory (RAM) to GPU memory.
   If your GPU memory size is 12 GB and RAM is 96 GB, set nLoads_gpu = 8.
   Increase this value if GPU error occurs (default: 8), do not change the default value otherwise.
   nSamples_gpu is now deprecated, and automatically calculated from nLoads_gpu parameter.

v3.2.2

[2017/12/30: v3.2.2]
Bugfix: PSTH histogram plot error is fixed and two PSTH plots are displayed
top and bottom when two units are selected.

v3.2.1

[2017/12/29: v3.2.1]
Old multishank probe file format is supported (v1, jrclust.m).
'cviShank' which is a cell containing a list of sites is converted to 'shank' format
FFT clean operation is faster now (used if "fft_clean" parameter is greater than 0)
Manual GUI: Number of spikes per unit displayed the x-axis label can be toggled by pressing 'n'
Manual GUI: performance improvement
Faster update when a unit is selected
Faster PSTH plot
Default log length decreased to 5 from 10 previously ('MAX_LOG' parameter).
New command: "jrc quality myparam.prm"
This command displays the unit quality info and exports to a csv file (ends with "_quality.csv").

v3.2.0

1. Bugfix for Manual GUI: unit selection cursors (black and red lines) do not disappear anymore after saving to a file.
   This has been an issue since v3.1.8 with an introduction of saving the
   cluster selection plot (rho vs. delta for the DPCLUS clustering algorithm).

2. Bugfix for "maketrial" command: supports binary files with header information and/or
   multiple combined recordings if multiple binary files are set in "csFile_merge" parameter.

3. Speed improvement for Manual GUI: "delete/merge/split" operation got significantly faster by removing unnecessary visual updates and text box display for the unit counts, which is now shown on the x-axis as "unit# (counts)". The text box indicating the unit count used to block the waveforms and took a long time to plot.

4. "jrc clear mybatch.batch" will clear the output of the .prm files listed the batch text file (.batch).

5. LFP-related commands are reintroduced from version 1 (jrclust.m)
   "jrc import-lfp" extracts LFP signal by subsampling the raw traces or by loading the LFP file (.imec.lf.bin) for Neuropixels recordings.
   LFP file name (.lfp.jrc) is automatically generated from .prm file and vcFile_lfp parameter is updated in .prm file.
   Subsampling is done by averaging the time bin (P.nSkip_lfp) to prevent aliasing as opposed to simply skipping samples.
   "jrc traces-lfp" plots the LFP traces with a larger time window by a factor of P.nSkip_lfp. This works similarly to "jrc traces" command for viewing wide-band traces.

v3.1.10

1. Manual GUI: Bugfix: Combination of selecting 'raw waveform' view in 'pca' unit works properly.

2. New parameter: 'nSamples_gpu' which sets the number of samples to be loaded to GPU memory.
   Current default is 250,000, and previous default was 1000,000 which could not be changed. Reduce this number if you run out of GPU memory. This value is used if P.fft_thresh > 0 or P.vcCommonRef=='whitening'.

3. Trace GUI: color of spikes remains consistent between time window switching.

4. Bugfix: Spikes near the beginning of the recordings are now properly merged (spkMerge_single_() function).

5. New options for common-mode rejection: 'vcCommonRef' now supports 'median' and 'whitening'. Setting vcCommonRef = 'whitening' will perform spatial whitening between channels.

6. New feature: "maketrial" command
   This function generates trial timestamps to plot PSTH (either rising or falling edges) and generates .mat file containing timestamps and sets 'vcFile_trial' field.
   For IMEC probes, use "maketrial-imec" to extract event input on the digital input pins (1-16). Specify the digital input channel by setting "dinput_imec_trial".

7. n-trode geometry is now supported (n>=1). You need to set each tetrode group as separate shanks by setting "shank" parameter in the .prb file for each site number.
   (e.g.) if site 1:4 belongs to tetrode 1 and site 5:8 belongs to tetrode 2, then set shank = [1 1 1 1 2 2 2 2];

8. New parameter: 'fSpatialMask_clu' is disabled by default (previously enabled). Spatial mask applies spatially decaying weight as a function of distance from the center site "maxDist_site_um" is used as the half-distance scale (1/2 weight is multiplied at that distance)
   Spatial masking is disabled if you have less than "min_sites_mask" number of sites per spiking events.

v3.1.9b

[2017/12/6: v3.1.9b]
This release correctly points to v3.1.9. Please do not download "v3.1.9" and "v3.1.9a".

v3.1.9a

This release correctly points to v3.1.9. The previous tag (v3.1.9) incorrectly pointed to v3.1.8.

v3.1.9

[2017/12/6: v3.1.9]
Bugfix: v3.1.8 incorrectly points to v3.1.7 on Github. Please download this version instead.
Bugfix: Opening previously sorted data (v3.1.1) to the latest vresion now works.
Parameter version upgrade function (upgrad_param_()) now handles new way to compute
maxSite and nSites_ref parameters.

v3.1.8

[2017/12/6: v3.1.8]
New feature: Rho-Delta plot is captured as .png file when _jrc.mat file is saved
Setting the parameter 'fSavePlot_RD = 0' will disable the figure capture (enabled by default).
You may adjust 'rho_cut' and 'delta1_cut' paramters based on the Rho-Delta plot.
Run 'jrc plot-rd' command to view the Rho-Delta plot.
Manual GUI
Unit position view displays number of spikes in a selected unit
Bugfix: Clusters with less than 6 spikes after manual splitting doesn't crash any more.
Bufix: Second manual splitting erases the first drawn polygon (splitting in the waveform view)
Bugfix: Switching between filtered and raw waveforms now use the same set of colors
Improved error reporting: "jrc_error_log.mat" records detailed error log.
Raw waveform duration is reverted back to 2 msec
spkLim_raw_factor = 2 (default) will use 2x of the time range (spkLim_ms) used for the filtered waveform
spkLim_factor_merge = 1 (default) will use 1x of the spkLim_ms (1 msec default) for the waveform based auto-merging
New default: maxDist_site_spk_um = 75 (changed from 70) for improved performance for probes with 25 um site spacing