Converting ABF1 files to NWB2

abf_to_nwb.py converts ABF v1 files to NWB v2 files.

Example:

Convert a step stimulus file to NWB by downloading the sample ABF file and executing the following command.

python3 abf_to_nwb.py data/abf1 --overwrite --acquisitionChannelName Iclamp --stimulusChannelName Current_in

The ABF v1 file and the output NWB v2 file can be found in data/abf1.

Note: "path/to/outputFolder" must not contain the output file.

Process

The conversion process as outlined in this repository is divided into a two-step process:

1. abf_to_nwb.py parses the specified input folder to create a list of ABF files, which are organized by cell.
2. The file(s) are passed into ABF1Converter.py which executes the conversion.

abf_to_nwb.py is generalized for the example conversion. It can be customized to collect lab-specific metadata for organizational purposes. The files white_noise_abf_to_nwb.py and cc_step_abf_to_nwb.py were written for the Toronto Western Hospital, and can be used as reference.

Specifications

• The script is customized for intracellular electrophysiology data collected during a patch clamp experiment through a single channel, without the presence of an external file containing amplifier settings.
• The data must be acquired by the Axon pClamp v9.2 software. Download pClamp 9

Validation

The resulting NWB v2 file can be validated in the following ways:

• Open the file using HDFView. Download HDFView
• Run create_nwb_pdf.py to create a PDF file with graphs that provide a visual representation of the data.
• Use the NWB Jupyter Widgets provided by Neurodata Without Borders. GitHub