Bug: Single channel ScanImage errors when channel_name is not specified

[h-mayorquin]

from neuroconv.datainterfaces import ScanImageImagingInterface
from pathlib import Path
import datetime as dt

file_path = Path("/Users/heberto/data/testing_data/ophys_testing_data/imaging_datasets/ScanImage/volumetric_single_channel_multi_file/vol_one_ch_multi_files_00001_00001.tif")
assert file_path.exists(), f"File path {file_path} does not exist."

date_time_now = dt.datetime.now()


interface = ScanImageImagingInterface(file_path=file_path, channel_name="")
metadata = interface.get_metadata()
metadata["NWBFile"]["session_start_time"] = date_time_now


nwbfile = interface.create_nwbfile(iterator_type=None, metadata=metadata)

Errors:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[11], [line 13](vscode-notebook-cell:?execution_count=11&line=13)
      9 date_time_now = dt.datetime.now()
     12 interface = ScanImageImagingInterface(file_path=file_path)
---> [13](vscode-notebook-cell:?execution_count=11&line=13) metadata = interface.get_metadata()
     14 metadata["NWBFile"]["session_start_time"] = date_time_now
     17 nwbfile = interface.create_nwbfile(iterator_type=None, metadata=metadata)

File ~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py:193, in ScanImageImagingInterface.get_metadata(self)
    191 device_name = "Microscope"
    192 metadata["Ophys"]["Device"][0].update(name=device_name, description=f"Microscope controlled by ScanImage")
--> [193](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/datainterfaces/ophys/scanimage/scanimageimaginginterfaces.py:193) channel_name_string = self.channel_name.replace(" ", "").capitalize()
    195 optical_channel_name = f"OpticalChannel{channel_name_string}"
    196 optical_channel_metadata = {
    197     "name": optical_channel_name,
    198     "description": "Optical channel from ScanImage acquisition",
    199     "emission_lambda": np.nan,
    200 }

AttributeError: 'NoneType' object has no attribute 'replace'

[h-mayorquin]

Another related error comes up even if specifying the channel related to transposing:

from neuroconv.datainterfaces import ScanImageImagingInterface
from pathlib import Path
import pynapple as nap
import datetime as dt

file_path = Path("/Users/heberto/data/testing_data/ophys_testing_data/imaging_datasets/ScanImage/volumetric_single_channel_multi_file/vol_one_ch_multi_files_00001_00001.tif")
assert file_path.exists(), f"File path {file_path} does not exist."

date_time_now = dt.datetime.now()


interface = ScanImageImagingInterface(file_path=file_path, channel_name="1")
metadata = interface.get_metadata()
metadata["NWBFile"]["session_start_time"] = date_time_now


nwbfile = interface.create_nwbfile(iterator_type=None, metadata=metadata)

[line 17](vscode-notebook-cell:?execution_count=13&line=17)ValueError: axes don't match array
[Hide Details](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/#!)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[13], [line 17](vscode-notebook-cell:?execution_count=13&line=17)
     13 metadata = interface.get_metadata()
     14 metadata["NWBFile"]["session_start_time"] = date_time_now
---> [17](vscode-notebook-cell:?execution_count=13&line=17) nwbfile = interface.create_nwbfile(iterator_type=None, metadata=metadata)
     19 data = nap.NWBFile(nwbfile)
     20 data

File ~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/basedatainterface.py:152, in BaseDataInterface.create_nwbfile(self, metadata, **conversion_options)
    149     metadata = self.get_metadata()
    151 nwbfile = make_nwbfile_from_metadata(metadata=metadata)
--> [152](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/basedatainterface.py:152) self.add_to_nwbfile(nwbfile=nwbfile, metadata=metadata, **conversion_options)
    154 return nwbfile

File ~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py:247, in BaseImagingExtractorInterface.add_to_nwbfile(self, nwbfile, metadata, photon_series_type, photon_series_index, parent_container, stub_test, stub_frames, always_write_timestamps, iterator_type, iterator_options, stub_samples)
    243     imaging_extractor = self.imaging_extractor
    245 metadata = metadata or self.get_metadata()
--> [247](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/datainterfaces/ophys/baseimagingextractorinterface.py:247) add_imaging_to_nwbfile(
    248     imaging=imaging_extractor,
    249     nwbfile=nwbfile,
    250     metadata=metadata,
    251     photon_series_type=photon_series_type,
    252     photon_series_index=photon_series_index,
    253     parent_container=parent_container,
    254     always_write_timestamps=always_write_timestamps,
    255     iterator_type=iterator_type,
    256     iterator_options=iterator_options,
    257 )

File ~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/tools/roiextractors/roiextractors.py:849, in add_imaging_to_nwbfile(imaging, nwbfile, metadata, photon_series_type, photon_series_index, iterator_type, iterator_options, parent_container, always_write_timestamps)
    814 """
    815 Add imaging data from an ImagingExtractor object to an NWBFile.
    816 
   (...)    846 
    847 """
    848 add_devices_to_nwbfile(nwbfile=nwbfile, metadata=metadata)
--> [849](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/tools/roiextractors/roiextractors.py:849) nwbfile = _add_photon_series_to_nwbfile(
    850     imaging=imaging,
    851     nwbfile=nwbfile,
    852     metadata=metadata,
    853     photon_series_type=photon_series_type,
    854     photon_series_index=photon_series_index,
    855     iterator_type=iterator_type,
    856     iterator_options=iterator_options,
    857     parent_container=parent_container,
    858     always_write_timestamps=always_write_timestamps,
    859 )
    861 return nwbfile

File ~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/tools/roiextractors/roiextractors.py:558, in _add_photon_series_to_nwbfile(imaging, nwbfile, metadata, photon_series_type, photon_series_index, parent_container, iterator_type, iterator_options, always_write_timestamps)
    555     photon_series_kwargs["dimension"] = imaging.get_sample_shape()
    557 # This adds the data in way that is memory efficient
--> [558](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/tools/roiextractors/roiextractors.py:558) imaging_extractor_iterator = _imaging_frames_to_hdmf_iterator(
    559     imaging=imaging,
    560     iterator_type=iterator_type,
    561     iterator_options=iterator_options,
    562 )
    563 photon_series_kwargs["data"] = imaging_extractor_iterator
    565 # Add timestamps or rate

File ~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/tools/roiextractors/roiextractors.py:787, in _imaging_frames_to_hdmf_iterator(imaging, iterator_type, iterator_options)
    785 if iterator_type is None:
    786     _check_if_imaging_fits_into_memory(imaging=imaging)
--> [787](https://file+.vscode-resource.vscode-cdn.net/Users/heberto/development/ccn-software-sfn-2025/notebooks/turner/~/development/ccn-software-sfn-2025/.venv/lib/python3.12/site-packages/neuroconv/tools/roiextractors/roiextractors.py:787)     return imaging.get_series().transpose((0, 2, 1))
    789 if iterator_type == "v1":
    790     warnings.warn(
    791         "iterator_type='v1' is deprecated and will be removed on or after March 2026. "
    792         "Use iterator_type='v2' for better chunking control and progress bar support.",
    793         FutureWarning,
    794         stacklevel=2,
    795     )

ValueError: axes don't match array