The NeuroFeatureExtract (NFE) gives the users the possibility to upload their own
experimental files from which to extract the electrophysiological features of interest.
Currently, two different formats are accepted for the upload: .abf and .json.
All uploaded files are remove from the server after the execution ended.
At runtime, they are only accessible to the user who uploaded them.
The upload functionality will be further extended in order to accept as many formats as possible
(e.g., all the formats readable by the
neo
software package).
ABF
The .abf format (i.e., Axon Binary Format), produced with Molecular Devices instruments, is supported. This file format is read though the neo package which is leveraged by the BluePyEfe package used in the NFE during the feature extraction process.In order to perform the feature extraction on this type of files, the user must upload both an .abf and a .json file containing the metadata concerning the .abf. The name of the metadata file must be the same as the .abf file with the metadata suffix (e.g. my_file.abf and my_file_metadata.json).
Here is an example of a .abf file and the corresponding .json metadata file: The metadata must contain the following fields, which give information on the step protocol used during the recordings (example values are given):
"stimulus_type": "step",
"stimulus_time_unit": "ms",
"stimulus_start": [639],
"stimulus_end": [1639],
"stimulus_unit": "nA",
"stimulus_first_amplitude": [-0.3],
"stimulus_increment": [0.05],
"sampling_rate_unit": "Hz",
"sampling_rate": [50000]
In particular, the "stimulus_first_amplitude" and the "stimulus_increment" indicate the amplitude of the stimulus release during the first sweep and the stimulus increment at every sweep (in case only one stimulus has been delivered the “stimulus_increment” must be set to 0). The web app expects the .abf file to contain the membrane voltage potential stored in the first AnalogSignal (following the neo software package nomenclature) and the stimulus trace in the second.
If you encounter any problem while uploading your files, contact us at: support [ AT ] ebrains.eu
JSON
The .json files are text files containing dictionaries base on key-value pairs. The accepted files are organized in such a way that, for each stimulus amplitude, the start and end time (indicated with the “tonoff” keys) and the voltage traces are reported in structured dictionaries. Here you can find a self-explanatory example file: json_example.json.If you encounter any problem while uploading your files, contact us at: support [ AT ] ebrains.eu