Dear Spikeinterface community,
I am asking for this feature in the _set_probes() as I would like to feed my previous dataset sorted by kilosort standalone into an analyser with the new function read_kilosort_as_analyzer #4366
The problem is that my probe map, coming from probe_interface library is not sorted by channels. While using spikeinterface to do spike sorting, it is fine to sort them by channels. However, when using read_kilosort_as_analyzer, it will check whether channels location used in the kilosort4 phy folder matches with its counterpart in the Recording (e.g. OpenEphysBinaryRecordingExtractor). Since kilosort4 does not sort the map, there is always a mismatch between the two.
or
I can certainly create a set of probe maps and sort them by channels first before using kilosort standalone to do spike sorting so that I will never to worry about this mismatch. However, would it be possible to make order = np.argsort(device_channel_indices) an option to skip so that both Recording and either my original probe.prb or kilosort's channel_map.npy, channel_locations.npy, and channel_shanks.npy are equally unsorted?
Or if you have any suggestion about circuvment the mismatch in channels location when using read_kilosort_as_analyzer?
Many thanks in advance.
Dear Spikeinterface community,
I am asking for this feature in the
_set_probes()as I would like to feed my previous dataset sorted by kilosort standalone into an analyser with the new functionread_kilosort_as_analyzer#4366The problem is that my probe map, coming from probe_interface library is not sorted by channels. While using spikeinterface to do spike sorting, it is fine to sort them by channels. However, when using
read_kilosort_as_analyzer, it will check whether channels location used in the kilosort4 phy folder matches with its counterpart in the Recording (e.g. OpenEphysBinaryRecordingExtractor). Since kilosort4 does not sort the map, there is always a mismatch between the two.or
I can certainly create a set of probe maps and sort them by channels first before using kilosort standalone to do spike sorting so that I will never to worry about this mismatch. However, would it be possible to make
order = np.argsort(device_channel_indices)an option to skip so that both Recording and either my original probe.prb or kilosort's channel_map.npy, channel_locations.npy, and channel_shanks.npy are equally unsorted?Or if you have any suggestion about circuvment the mismatch in channels location when using
read_kilosort_as_analyzer?Many thanks in advance.