[Bug]: How to insert channel location data into nwb file?

[Auxcy1ene]

What happened?

For my MSci project I am required to analyse many recordings of electrophysiology data. Unfortunately all of this data has apparently been recorded using a device from Axion Biosystems. This sucks because neither spike interface, nor any other spike sorting algorithm appears to natively support the importing of data recorded from this device. To further complicate things I have to use kilosort 3 for my project. I have spent an awful long time trying to get this data into ANY spike sorting program with no success whatsoever. Recently however, I have happened across the Neurodata Without Borders filetype, which just so happened to be an accepted filetype for spike interface (which is the main software I am using). The only problem is that when I was manuall building the nwb file using the tutorial available here (https://pynwb.readthedocs.io/en/stable/tutorials/domain/ecephys.html#sphx-glr-tutorials-domain-ecephys-py). It should also be noted that the files that Axion Biosystems devices produces are kind of unusual and require their own set of matlab functions to get any usable data out of it (see the guide pdf here:
AxionBioSystems_Matlab_guide.pdf
and the zip of functions I was provided with are here:
OneDrive_1_11-09-2024.zip). If I remember correctly there might be some gui software that could convert this filetype to a different filetype but it requires an undisclosed amount of money for the license (which is of course completely prohibitive for me) so I have to find a way of running this data through kilosort on my own. After coming across the tutorial on how to create a nwb file from scratch I immediately wrote a script to generate files for my own project as I was aware that spike interface accepted nwb files however when I tried to run it through kilosort via spike interface I was given the error that there were no channel locations stated in the file. After looking for a while I was unable to find anything that would allow me to insert channel location data into a nwb file, so finally the question I ask you is this:
Is there anyway I can insert channel location data into a nwb file, and if not how do I convert the nwb file to a different filetype where I can insert channel location data (since I have looked around and cannot find any tools for converting from an nwb filetype, instead I have only found tools for converting to the nwb filetype)?
Many Thanks in advance
From Sean

Steps to Reproduce

I cannot insert channel location data into my nwb file.

Traceback

No response

Operating System

Windows

Python Executable

Conda

Python Version

3.11

Package Versions

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nano==0.10.0
natsort==8.4.0
navigator-updater @ file:///C:/b/abs_22_3uaq2ey/croot/navigator-updater_1718030405023/work
nbclient @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/nbclient_1701796752236/work
nbconvert @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/nbconvert_1701806279884/work
nbformat @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/nbformat_1701796704118/work
ndx-grayscalevolume==0.0.2
ndx-icephys-meta==0.1.0
ndx-spectrum==0.2.2
neo==0.13.3
nest-asyncio @ file:///C:/b/abs_65d6lblmoi/croot/nest-asyncio_1708532721305/work
networkx @ file:///C:/b/abs_3bxnu56g9d/croot/networkx_1717597507456/work
nltk @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/nltk_1699503238228/work
notebook @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/notebook_1709157811033/work
notebook_shim @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/notebook-shim_1701806592322/work
numba @ file:///C:/b/abs_3d6x7o_csg/croot/numba_1712006672408/work
numcodecs==0.13.0
numexpr @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/numexpr_1699503421264/work
numpy @ file:///C:/b/abs_c1ywpu18ar/croot/numpy_and_numpy_base_1708638681471/work/dist/numpy-1.26.4-cp312-cp312-win_amd64.whl#sha256=becc06674317799ad0165a939a7613809d0bee9bd328a1e4308c57c39cacf08c
numpydoc @ file:///C:/b/abs_bbspp5l8vu/croot/numpydoc_1718279185573/work
nwb-conversion-tools==0.11.38
nwb-web-gui @ file:///C:/Users/sean_/Documents/nwb-web-gui
nwbinspector==0.5.2
nwbwidgets==0.10.2
openpyxl @ file:///C:/b/abs_764brjadj1/croot/openpyxl_1714158895873/work
overrides @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/overrides_1701806336503/work
packaging @ file:///C:/b/abs_cc1h2xfosn/croot/packaging_1710807447479/work
pandas @ file:///C:/b/abs_9aotnvvz16/croot/pandas_1718308978393/work/dist/pandas-2.2.2-cp312-cp312-win_amd64.whl#sha256=93959056e02e9855025011adb18394296a58d49e72b9342733b7693a5267c790
pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work
panel @ file:///C:/b/abs_aa_7bchst1/croot/panel_1718119034279/work
param @ file:///C:/b/abs_52u4gplvtg/croot/param_1711136867369/work
paramiko @ file:///opt/conda/conda-bld/paramiko_1640109032755/work
parsel @ file:///C:/b/abs_ebc3tzm_c4/croot/parsel_1707503517596/work
parso @ file:///opt/conda/conda-bld/parso_1641458642106/work
partd @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/partd_1699482661603/work
pathspec @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pathspec_1699472481068/work
patsy @ file:///C:/b/abs_21hy_wyj13/croot/patsy_1718378184379/work
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
pillow @ file:///C:/b/abs_95ls_qh4c2/croot/pillow_1714398870615/work
pkce @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pkce_1699482718905/work
pkginfo @ file:///C:/b/abs_bciypal17m/croot/pkginfo_1715696027839/work
platformdirs @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/platformdirs_1701797392447/work
plotly @ file:///C:/b/abs_9asyl7560v/croot/plotly_1718136949929/work
pluggy @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pluggy_1699472504117/work
ply @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/ply_1699473999871/work
probeinterface==0.2.23
prometheus-client @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/prometheus_client_1699495496669/work
prompt-toolkit @ file:///C:/b/abs_68uwr58ed1/croot/prompt-toolkit_1704404394082/work
Protego @ file:///tmp/build/80754af9/protego_1598657180827/work
protobuf==3.20.3
psutil @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/psutil_1699482842340/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work
py-cpuinfo @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/py-cpuinfo_1699495567147/work
py2vega==0.6.1
pyarrow @ file:///C:/b/abs_93i_y2dub4/croot/pyarrow_1707330894046/work/python
pyasn1 @ file:///Users/ktietz/demo/mc3/conda-bld/pyasn1_1629708007385/work
pyasn1-modules==0.2.8
pycodestyle @ file:///C:/b/abs_e9pt4mahct/croot/pycodestyle_1701910643139/work
pycosat @ file:///C:/b/abs_5csdern___/croot/pycosat_1714513102923/work
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
pycryptodomex==3.20.0
pyct @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pyct_1699542988857/work
pycurl==7.45.2
pydantic @ file:///C:/b/abs_f6ffn86wjx/croot/pydantic_1709578044014/work
pydantic_core @ file:///C:/b/abs_05smrkbwjm/croot/pydantic-core_1709574000211/work
pydeck @ file:///C:/b/abs_ad9p880wi1/croot/pydeck_1706194121328/work
PyDispatcher @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pydispatcher_1699543033434/work
pydocstyle @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pydocstyle_1699495611004/work
pyerfa @ file:///C:/b/abs_477fivsfe8/croot/pyerfa_1717700768172/work
pyflakes @ file:///C:/b/abs_b6t1aazq2e/croot/pyflakes_1708963020907/work
Pygments @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pygments_1699474141968/work
PyJWT @ file:///C:/b/abs_04qhgo75wz/croot/pyjwt_1715095119685/work
pylint @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pylint_1699495689806/work
pylint-venv @ file:///C:/b/abs_3f6p_17zia/croot/pylint-venv_1709837680309/work
pyls-spyder==0.4.0
PyNaCl @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pynacl_1699563077212/work
pynwb==2.8.1
pyodbc @ file:///C:/b/abs_90kly0uuwz/croot/pyodbc_1705431396548/work
pyopenephys==1.2.0
pyOpenSSL @ file:///C:/b/abs_5449ditk12/croot/pyopenssl_1708386245896/work
pyout==0.7.3
pyparsing @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pyparsing_1699476875614/work
PyQt5==5.15.10
PyQt5-sip @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pyqt-split_1699478669290/work/pyqt_sip
pyqtgraph==0.13.7
PyQtWebEngine==5.15.6
PySocks @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pysocks_1699473336188/work
pytest @ file:///C:/b/abs_een_3z747j/croot/pytest_1717793253670/work
python-dateutil @ file:///C:/b/abs_3au_koqnbs/croot/python-dateutil_1716495777160/work
python-dotenv @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/python-dotenv_1699475097728/work
python-json-logger @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/python-json-logger_1699543626759/work
python-lsp-black @ file:///C:/b/abs_5dhen_5vga/croot/python-lsp-black_1709232962589/work
python-lsp-jsonrpc @ file:///croot/python-lsp-jsonrpc_1708962872556/work
python-lsp-server @ file:///C:/b/abs_2cdyzvcq4z/croot/python-lsp-server_1708971796975/work
python-slugify @ file:///tmp/build/80754af9/python-slugify_1620405669636/work
python-snappy @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/python-snappy_1699564939880/work
pythreejs==2.4.2
pytoolconfig @ file:///C:/b/abs_f2j_xsvrpn/croot/pytoolconfig_1701728751207/work
pytz @ file:///C:/b/abs_6ap4tsz1ox/croot/pytz_1713974360290/work
pyviz_comms @ file:///C:/b/abs_674gfmqoxa/croot/pyviz_comms_1711136872853/work
pywavelets @ file:///C:/b/abs_7est386xsb/croot/pywavelets_1705049855879/work
pywin32==305.1
pywin32-ctypes @ file:///C:/b/abs_2cfx5l4nvi/croot/pywin32-ctypes_1709340246092/work
pywinpty @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pywinpty_1699496010557/work/target/wheels/pywinpty-2.0.10-cp312-none-win_amd64.whl#sha256=227f3f94f568f63ab3418c02875c4b429a0a3638e1a2917a22bb8e4ba1762179
PyYAML @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/pyyaml_1699479991712/work
pyzmq @ file:///C:/b/abs_89aq69t0up/croot/pyzmq_1705605705281/work
QDarkStyle @ file:///croot/qdarkstyle_1709231003551/work
qstylizer @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/qstylizer_1699565338341/work/dist/qstylizer-0.2.2-py2.py3-none-any.whl#sha256=be2f7d956d89710f13dee80f2d594e794c2710f12576fe60ecee84dd1ad72180
QtAwesome @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/qtawesome_1699565380106/work
qtconsole @ file:///C:/b/abs_03f8rg9vl6/croot/qtconsole_1709231218069/work
QtPy @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/qtpy_1701807198514/work
quantities==0.15.0
queuelib @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/queuelib_1699543858829/work
referencing @ file:///C:/Users/dev-admin/py312/referencing_1706802962559/work
regex @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/regex_1699483134599/work
requests @ file:///C:/b/abs_9c5n24p1y7/croot/requests_1716902867639/work
requests-file @ file:///Users/ktietz/demo/mc3/conda-bld/requests-file_1629455781986/work
requests-toolbelt @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/requests-toolbelt_1699475466775/work
retrying==1.3.4
rfc3339-validator @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/rfc3339-validator_1699543924991/work
rfc3986-validator @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/rfc3986-validator_1699543955651/work
rfc3987==1.3.8
rich @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/rich_1699475515016/work
roiextractors==0.4.17
rope @ file:///C:/b/abs_a4uy0nuc8z/croot/rope_1708963217026/work
rpds-py @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/rpds-py_1699565648947/work
Rtree @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/rtree_1699565751755/work
ruamel-yaml-conda @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/ruamel_yaml_1699543990032/work
ruamel.yaml @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/ruamel.yaml_1699483184324/work
s3fs @ file:///C:/b/abs_972cxni1lb/croot/s3fs_1714466090144/work
scikit-image @ file:///C:/b/abs_c8fk8452if/croot/scikit-image_1718285241274/work
scikit-learn @ file:///C:/b/abs_d6_krvz8aa/croot/scikit-learn_1714164798159/work
scipy @ file:///C:/b/abs_efv75hqhju/croot/scipy_1717521501389/work/dist/scipy-1.13.1-cp312-cp312-win_amd64.whl#sha256=b29dba691773ea983857b31cad894f31623348583937b6f03783facfd7abc734
Scrapy @ file:///C:/b/abs_b407wrcuij/croot/scrapy_1708714755460/work
seaborn @ file:///C:/b/abs_ca2mi1rgmn/croot/seaborn_1718303534355/work
semantic-version==2.10.0
semver @ file:///C:/b/abs_4bkbn3v6jp/croot/semver_1709243682483/work
Send2Trash @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/send2trash_1701806400767/work
service-identity @ file:///Users/ktietz/demo/mc3/conda-bld/service_identity_1629460757137/work
setuptools==69.5.1
sip @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/sip_1699475590677/work
six @ file:///tmp/build/80754af9/six_1644875935023/work
smart-open @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/smart_open_1699483216058/work
smmap @ file:///tmp/build/80754af9/smmap_1611694433573/work
sniffio @ file:///C:/b/abs_3akdewudo_/croot/sniffio_1705431337396/work
snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1637937080595/work
sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1623949099177/work
soupsieve @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/soupsieve_1699496611169/work
Sphinx @ file:///C:/b/abs_67j2y1kkd0/croot/sphinx_1718275396111/work
sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work
sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work
sphinxcontrib-htmlhelp @ file:///tmp/build/80754af9/sphinxcontrib-htmlhelp_1623945626792/work
sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work
sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work
sphinxcontrib-serializinghtml @ file:///C:/b/abs_91266tdnkr/croot/sphinxcontrib-serializinghtml_1718201501959/work
spikeextractors==0.9.11
spikeinterface==0.101.0
spyder @ file:///C:/b/abs_a2orhmqnuf/croot/spyder_1710523737931/work
spyder-kernels @ file:///C:/b/abs_e5u6y4ldr2/croot/spyder-kernels_1707937767956/work
SQLAlchemy @ file:///C:/b/abs_aa2izo0xio/croot/sqlalchemy_1718378184063/work
stack-data @ file:///opt/conda/conda-bld/stack_data_1646927590127/work
statsmodels @ file:///C:/b/abs_54b33xdukx/croot/statsmodels_1718381209933/work
streamlit @ file:///C:/b/abs_12o66j0das/croot/streamlit_1710262558078/work
sympy @ file:///C:/b/abs_82njkonm7f/croot/sympy_1701397685028/work
tables @ file:///C:/b/abs_411740ajo7/croot/pytables_1705614883108/work
tabulate @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/tabulate_1701812852133/work
tblib @ file:///Users/ktietz/demo/mc3/conda-bld/tblib_1629402031467/work
tenacity @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/tenacity_1699483390626/work
terminado @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/terminado_1699545066607/work
text-unidecode @ file:///Users/ktietz/demo/mc3/conda-bld/text-unidecode_1629401354553/work
textdistance @ file:///tmp/build/80754af9/textdistance_1612461398012/work
threadpoolctl==3.5.0
three-merge @ file:///tmp/build/80754af9/three-merge_1607553261110/work
tifffile @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/tifffile_1699496794322/work
tinycss2 @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/tinycss2_1699545185754/work
tldextract @ file:///opt/conda/conda-bld/tldextract_1646638314385/work
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
tomli @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/tomli_1699472528897/work
tomlkit @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/tomlkit_1699475633229/work
toolz @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/toolz_1699474617784/work
torch==2.4.1
tornado @ file:///C:/b/abs_7bua0304mj/croot/tornado_1718740122405/work
tqdm @ file:///C:/b/abs_a7h7n45ccq/croot/tqdm_1716395987133/work
traitlets @ file:///C:/b/abs_bfsnoxl4pq/croot/traitlets_1718227069245/work
traittypes==0.2.1
trimesh==4.4.9
truststore @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/truststore_1701881385424/work
Twisted @ file:///C:/b/abs_e7yqd811in/croot/twisted_1708702883769/work
twisted-iocpsupport @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/twisted-iocpsupport_1699496891011/work
typing_extensions @ file:///C:/b/abs_0as9mdbkfl/croot/typing_extensions_1715268906610/work
tzdata @ file:///croot/python-tzdata_1690578112552/work
uc-micro-py @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/uc-micro-py_1699545612984/work
ujson @ file:///C:/b/abs_c93a278xy4/croot/ujson_1717598062082/work
unicodedata2 @ file:///C:/b/abs_b6apldlg7y/croot/unicodedata2_1713212998255/work
Unidecode @ file:///tmp/build/80754af9/unidecode_1614712377438/work
uri-template==1.3.0
urllib3 @ file:///C:/b/abs_a7hvzm4y95/croot/urllib3_1718912661242/work
voila==0.5.7
w3lib @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/w3lib_1709162573908/work
watchdog @ file:///C:/b/abs_b3l_3s276z/croot/watchdog_1717166538403/work
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webcolors==24.8.0
webencodings @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/webencodings_1699497069416/work
websocket-client @ file:///C:/b/abs_5dmnxxoci9/croot/websocket-client_1715878351319/work
websockets==13.0.1
Werkzeug @ file:///C:/b/abs_8bittcw9jr/croot/werkzeug_1716533366070/work
whatthepatch @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/whatthepatch_1699497134590/work
wheel==0.43.0
widgetsnbextension==4.0.13
win-inet-pton @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/win_inet_pton_1699472992992/work
wrapt @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/wrapt_1699480231633/work
xarray @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/xarray_1699480274069/work
xlwings @ file:///C:/b/abs_6bsaqa795f/croot/xlwings_1718046948745/work
xmltodict==0.13.0
xyzservices @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/xyzservices_1699548906163/work
yapf @ file:///C:/b/abs_8aidayep18/croot/yapf_1708964372649/work
yarl @ file:///C:/b/abs_8bxwdyhjvp/croot/yarl_1701105248152/work
zarr==2.17.2
zict @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/zict_1699548979005/work
zipp @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/zipp_1707493775475/work
zope.interface @ file:///C:/Users/dev-admin/perseverance-python-buildout/croot/zope.interface_1699497164709/work
zstandard @ file:///C:/b/abs_e46tf0_91g/croot/zstandard_1714678303615/work
Note: you may need to restart the kernel to use updated packages.

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?