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spikeglxrawio.py updated to support 1.0-NHP probes #1237

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Merged
merged 4 commits into from
Mar 22, 2023
Merged

spikeglxrawio.py updated to support 1.0-NHP probes #1237

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419a8bb
spikeglxrawio.py updated to support 45mm 1.0-NHP probes
NDolensek Mar 22, 2023
604c4f3
added NP 1.0-NHP short and medium length support
NDolensek Mar 22, 2023
a234723
added imDatPrb_type=1031 support as per SpikeGLX source
NDolensek Mar 22, 2023
d4dae04
improved 1.0-NHP probe docs
NDolensek Mar 22, 2023
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9 changes: 7 additions & 2 deletions neo/rawio/spikeglxrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,11 @@
imDatPrb_type=1 (NP 1.0)
imDatPrb_type=21 (NP 2.0, single multiplexed shank)
imDatPrb_type=24 (NP 2.0, 4-shank)
imDatPrb_type=1030 (NP 1.0-NHP 45mm SOI90 - NHP long 90um wide, staggered contacts)
imDatPrb_type=1031 (NP 1.0-NHP 45mm SOI125 - NHP long 125um wide, staggered contacts)
imDatPrb_type=1032 (NP 1.0-NHP 45mm SOI115 / 125 linear - NHP long 125um wide, linear contacts)
imDatPrb_type=1022 (NP 1.0-NHP 25mm - NHP medium)
imDatPrb_type=1015 (NP 1.0-NHP 10mm - NHP short)

Author : Samuel Garcia
Some functions are copied from Graham Findlay
Expand Down Expand Up @@ -380,7 +385,7 @@ def extract_stream_info(meta_file, meta):
# metad['imroTbl'] contain two gain per channel AP and LF
# except for the last fake channel
per_channel_gain = np.ones(num_chan, dtype='float64')
if 'imDatPrb_type' not in meta or meta['imDatPrb_type'] == '0':
if 'imDatPrb_type' not in meta or meta['imDatPrb_type'] == '0' or meta['imDatPrb_type'] in ('1015', '1022', '1030', '1031', '1032'):
# This work with NP 1.0 case with different metadata versions
# https://github.com/billkarsh/SpikeGLX/blob/gh-pages/Support/Metadata_3A.md#imec
# https://github.com/billkarsh/SpikeGLX/blob/gh-pages/Support/Metadata_3B1.md#imec
Expand All @@ -404,7 +409,7 @@ def extract_stream_info(meta_file, meta):
channel_gains = gain_factor * per_channel_gain * 1e6
else:
raise NotImplementedError('This meta file version of spikeglx'
'is not implemented')
' is not implemented')
else:
stream_kind = ''
stream_name = device
Expand Down