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Convert various patch-clamp data formats to NWBv2

Project description

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Converting ABF/DAT files to NWB

The script 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)

ABF specialities

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.

Examples

Convert a single file
x-to-nwb 2018_03_20_0000.abf
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

Disabling compression

The following command disables compression of the HDF5 datasets (intended for debugging purposes).

x-to-nwb --no-compression 2018_03_20_0000.abf

DAT specialities

Required input files

DAT files acquired with Patchmaster version 2x90.

Examples

Convert a single file creating one NWB file per Group
x-to-nwb H18.28.015.11.12.dat
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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Files for x-to-nwb, version 0.2.1
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