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cortex-lab / phy

phy: interactive visualization and manual spike sorting of large-scale ephys data
BSD 3-Clause "New" or "Revised" License
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Shank visualization #1262

Open MFalappa opened 6 months ago

MFalappa commented 6 months ago

Hello, I am an engineer at Corticale and I am using Phy on some data collected with our probes.

Currently, I am analyzing data from a probe with 8 shanks (2 columns and 64 rows for each shank, for a total of 1024 channels). if I have understood correctly, it seems that traces from the same shank have the same color, but they are not contiguous as they are organized by depth. I was wondering if it would be possible to organize the channels in TraceView not only by depth but also by index, or at least to organize the traces so that those belonging to the same shank are contiguous.

thanks in advances

phy_8s

MFalappa commented 6 months ago

In the meantime, in TraceView class, I changed self.channel_y_ranks = np.argsort(np.argsort(self.channel_positions[:, 1])) to self.channel_y_ranks = np.arange(self.channel_positions.shape[0], dtype='int64')[::-1], but it would be good if it is possible switching between the two visualization in the gui

zm711 commented 5 months ago

They should. If a channel is next to another channel on the same shank phy will automatically display them next to each other. If it is not there is one of the two things 1) confusion about the channel contact vs the data number (ie an electrode might be number 1, but might come from data row 10 so phy will list it as 10 not 1) 2) the channel map was made wrong.