Convert various patch-clamp data formats to NWBv2
Converting ABF/DAT files to NWB
x-to-nwb allows to convert ABF/DAT files to NeurodataWithoutBorders v2 files.
For programmatic use the function
convert is designed as public interface.
from x_to_nwb import convert help(convert)
As of 9/2018 PClamp/Clampex does not record all required amplifier settings.
For gathering these please see the
mcc_get_settings.py script in the ipfx
repository which gathers all amplifier settings from all active amplifiers and
writes them to a file in JSON output.
In case you don't have a JSON settings file pass
--no-searchSettingsFile to avoid warnings.
By default all AD and DA channels are outputted into the NWB file. You can select to only export some AD channels with
x-to-nwb --includeChannel ABCD 2018_03_20_0000.abf
Or to discard some AD channels use
x-to-nwb --discardChannel ABCD 2018_03_20_0000.abf
Required input files
- ABF files acquired with Clampex/pCLAMP.
- If custom waveforms are used for the stimulus protocol, the source ATF files are required as well.
Convert a single file
Convert a single file with overwrite and use a directory for finding custom waveforms
Some acquired data might use custom wave forms for defining the stimulus protocols. These custom waveforms are stored in external files and don't reside in the ABF files. We therefore allow the user to pass a directory where these files should be searched. Currently only custom waveforms in ATF (Axon Text format) are supported.
x-to-nwb --overwrite --protocolDir protocols 2018_03_20_0000.abf
Convert a folder with ABF files
The following command converts all ABF files which reside in
someFolder to a single NWB file.
x-to-nwb --fileType ".abf" --overwrite someFolder
The following command disables compression of the HDF5 datasets (intended for debugging purposes).
x-to-nwb --no-compression 2018_03_20_0000.abf
Required input files
DAT files acquired with Patchmaster version 2x90.
Convert a single file creating one NWB file per Group
Convert a single file creating one NWB file with all Groups
x-to-nwb --multipleGroupsPerFile H18.28.015.11.12.dat
Outputting DAT/ABF metadata files for debugging purposes
x-to-nwb --outputMetadata *.dat *.abf
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