I'm having an issue with a discrepancy with the max spike locations in the HS2 output vs the actual size of the MEA. The MEA is a 64 x 64 grid and the electrodes are 21um x 21um with a pitch of 60um and the total size is 3801um. However, the max x,y locations of the output spikes is always only 3780 for both X and Y and you can see a distinct line where spikes seem to appear to be at the edge of the MEA even though they should extend all the way to 3801. The minimum value is 0 for X and Y indicating that it is correctly detecting spikes for the electrodes in the first row and column on the MEA, but it is either not detecting spikes for the last row and column or everything is being scaled down 21um. If I look at the channel assignment for the detected units, it does seem to detect units on electrodes in the last row and column, so I am concerned everything is being scaled down location wise.
Any ideas for what might be causing this and how to fix it? Thanks for your support and let me know if you need any more information.
(I am using HS2 3.104 as we still have issues with HS2 4 detecting too many spikes in our dataset).
recording1 = se.read_biocam('/home/exacloud/gscratch/Sivyerlab/Primate_040924/040924_Macula_OD_OS_ND3_00.brw', mea_pitch=60, electrode_width=21)
recording2 = se.read_biocam('/home/exacloud/gscratch/Sivyerlab/Primate_040924/040924_Macula_OD_OS_ND2_01.brw', mea_pitch=60, electrode_width=21)
recording_list = [recording1, recording2]
recording_concatenated = si.concatenate_recordings(recording_list)
sorter_params = {
"clustering_bandwidth": 20,
"clustering_alpha": 5.5,
"clustering_n_jobs": -1,
"clustering_bin_seeding": True,
"clustering_min_bin_freq": 16,
"clustering_subset": None,
"left_cutout_time": 0.3,
"right_cutout_time": 1.8,
"detect_threshold": 20,
# extra probe params
"probe_masked_channels": [],
"probe_inner_radius": 100,
"probe_neighbor_radius": 129,
"probe_event_length": 0.26,
"probe_peak_jitter": 0.2,
# extra detection params
"t_inc": 100000,
"num_com_centers": 1,
"maa": 12,
"ahpthr": 11,
"out_file_name": "HS2_detected",
"decay_filtering": False,
"save_all": False,
"amp_evaluation_time": 0.4,
"spk_evaluation_time": 1.0,
# extra pca params
"pca_ncomponents": 2,
"pca_whiten": True,
# bandpass filter
"freq_min": 300.0,
"freq_max": 6000.0,
"filter": True,
# rescale traces
"pre_scale": True,
"pre_scale_value": 20.0,
# remove duplicates (based on spk_evaluation_time)
"filter_duplicates": True,}
sorting = ss.run_sorter(sorter_name="herdingspikes", recording=recording_concatenated, **sorter_params)
I'm having an issue with a discrepancy with the max spike locations in the HS2 output vs the actual size of the MEA. The MEA is a 64 x 64 grid and the electrodes are 21um x 21um with a pitch of 60um and the total size is 3801um. However, the max x,y locations of the output spikes is always only 3780 for both X and Y and you can see a distinct line where spikes seem to appear to be at the edge of the MEA even though they should extend all the way to 3801. The minimum value is 0 for X and Y indicating that it is correctly detecting spikes for the electrodes in the first row and column on the MEA, but it is either not detecting spikes for the last row and column or everything is being scaled down 21um. If I look at the channel assignment for the detected units, it does seem to detect units on electrodes in the last row and column, so I am concerned everything is being scaled down location wise.
Any ideas for what might be causing this and how to fix it? Thanks for your support and let me know if you need any more information.
(I am using HS2 3.104 as we still have issues with HS2 4 detecting too many spikes in our dataset).
I am using SpikeInterface and set up my parameters as follows