Probe file

Parameters in the probe file (.prb)

Supplied probe files are stored in ./prb/ folder in JRCLUST  

Example probe file

• Probe file (.prb) follows a Matlab syntax. Matlab uses [ ] to define arrays and matrices. You can separate matrix elements by space, tab or comma, and create a new row by using ;. For example [1 2; 3 4; 5 6] creates a 3x2 matrix (3 rows and 2 columns). The equivalent syntax is [1, 2; 3, 4; 5, 6] or [1 2; 3, 4; 5 6].

% Order of the probe sites in the recording file
channels = 1 + [40  103 39	104	41	102	38	105	42	101	37	106	43	100	36	107 44	99	35	108	45	98	34	109	46	97	33	110	47	96	32	111 48	127	63	112	49	126	62	113	50	125	61	114	51	124	60	115 52	116	59	123	53	117	58	122	54	118	57	121	55	119	56	120 8	71	7	72	9	70	6	73	10	74	5	69	11	75	4	68 12	76	3	67	13	77	2	66	14	78	1	65	15	79	0	64 16	80	31	95	17	81	30	94	18	82	29	93	19	83	28	92     20	84	27	91	21	85	26	90	22	86	25	89	23	87	24	88];

% Site location in micrometers (x and y)   
geometry = zeros(128, 2);    % Create a 128 x 2 matrix filled with zero
geometry(1:2:end,1) = 0;     % Set the x-coordinates of the left-edge sites
geometry(2:2:end,1) = 28;    % Set the x-coordinates of the right-edge sites
geometry(1:2:end,2) = 20*(0:63);    % Set the y-coordinates of the left-edge sites
geometry(2:2:end,2) = geometry(1:2:end,2); % Set the y-coordinates of the right edge sites by copying the left-edge site values

% Reference sites are being excluded  
ref_sites = [1 18 33 50 65 82 97 114]; % Specify the site numbers to exclude
channels(ref_sites) = [];  % Delete reference sites from the channels vector
geometry(ref_sites,:) = []; % Delete reference sites from the geometry matrix

% Recording contact pad size in micrometers. Height x width
pad = [12 12];

% Default prm
maxSite = 4.5;    % Used to calculate the number of sites to group spikes (nSites_spk = 1 + maxSite*2)
um_per_pix = 20;  % Vertical site center-to-center spacing (used for display)

% Shank information
shank = ones(size(channels));  % All sites belong to shank 1 (single shank recording)

Tags (variable names)

• channels: dimension: (1 x nSites), where nSites is the number of sites to load
  It contains a list of channel numbers in the recording file. 1 is added to translate 0-base in C to 1-base index used in Matlab. The channels are ordered by the physical site locations. The sites are ordered from the bottom to top, left to right. For example, the first element in the “channels” array corresponds to the bottom left site, the second element corresponds to the bottom right sites, the third element corresponds to the second bottom left site, and the last element corresponds to the top right site.

• geometry: dimension: (nSites x 2)
  Location of each site in micrometers. The first column corresponds to the width dimension and the second column corresponds to the depth dimension (parallel to the probe shank).

• pad: dimension: (1 x 2)
  Dimensions of a rectangular recording site: [height, width] in micrometers.

• ref_sites: dimension: (1 x k) where k is the number of reference sites (optional)
  This indicates reference or disconnected sites to eliminate.

• shank: dimension: (1 x nSites) (optional for single-shank probes)
  Shank number for each site #. For example shank=[1,1,1,1,2,2,2,2] will assign sites 1-4 to shank 1 and sites 5-8 to shank 2. It has the same dimension as the channels.

• maxSite: scalar (optional to set the probe-specific default setting)
  Number of neighboring sites in each direction to extract spike waveforms (see “Parameter settings” section)

• nSites_ref: scalar (optional to set the probe-specific default setting)
  Total number of reference sites to exclude for feature extraction (see “Parameter settings” section)

• um_per_pix: scalar (optional)
  Micrometers per center-to-center vertical site spacing

Visualizing the probe file

• Run jrc probe sample.prb to plot the probe layout for sample.prb
• See also: Probe-GUI