AxionFileLoader

This repository contains Matlab loaders for Axion BioSystem's AxIS and AxIS Navigator files. It enables extraction of raw voltage, spike times and waveforms, viability, contractility data, and stimulation timing from Axion's .raw and .spk files.

Example usage

Voltage data from a raw file

Voltage data is loaded in as a 4-D channel array structure. Data is indexed as well row, well column, electrode column, electrode row.

%load all voltage data
Data = AxisFile(‘Filename.raw’).RawVoltageData.LoadData; 
%Alternatively, load voltage data from Well A2 Electrode 31 from 10 s to 30 s
Data = AxisFile(‘Filename.raw’).RawVoltageData.LoadData(‘A2’,’31’,[10 30]);

Then, isolate the properly scaled data of interest.

[time,voltage] = Data{1,2,3,1}.GetTimeVoltageVector; %well A2 electrode 31

Contractility data from a raw file figure

Contractility data is loaded in as a 4-D channel array structure. Data is indexed as well row, well column, electrode column, electrode row.

%load all voltage data
Data = AxisFile(‘Filename.raw’).RawContractilityData.LoadData; 
%Alternatively, load voltage data from Well E4 Electrode 12 from 120 s to 180 s
Data = AxisFile(‘Filename.raw’).RawContractilityData.LoadData(‘E4’,’12’,[120 180]);

Then, isolate the properly scaled data of interest.

[time,contrac] = Data{5,4,3,1}.GetTimeVoltageVector;

Spike times and waveforms from a spk file

Spike timing, channel location, and waveforms are all stored in .spk files.

%load all spike data
Data = AxisFile(‘Filename.spk’).SpikeData.LoadData;

Then, isolate the properly scaled data of interest.

spikeTimes = [Data{3,2,2,1}(:).Start]; %all spike times in Well B2 Electrode 21
spikeWaveform = Data{3,2,2,1}(1).GetVoltageVector; %spike waveform of the 1st spike on Well B2 Electrode 21

Stimulation tag timing

Note that timestamps are only available if your stimulation included a tag (inverted triangle). A tag is automatically included for Brain and Heart pre-configured blocks.

Data = AxisFile('Filename.raw'); 
evts = sort([Data.StimulationEvents(:).EventTime]);

For more details, please refer to the Wiki.

Current Version

This release (1.1.0.0) was released alongside AxIS 3.7.1 and is the most current version.

Changelog

[1.1.0.0] - 2022-10-14

Released alongside AxIS 3.7.1

Added

Added support for files recorded in the new Neural Broadband mode
Added Duration field to the headers to indicate duration (in seconds) of the data set.

[1.0.0.0]

Initial public release!

krhe / axionfileloader Goto Github PK