ABF, or Axon Binary Format, is the format of files created by data acquisition programs from Axon Instruments, Inc.
reads files generated by several packages from Axon Instruments, Inc:
| Vendor | Package | Version |
|---|---|---|
| Axon Instruments, Inc. | pClamp | 6, 7, 8, 9 |
| Axon Instruments, Inc. | AxoScope | 1, 8, 9 |
| Axon Instruments, Inc. | AxoTape | 2 |
The filter does not support files generated by pClamp 5.x, since these files are not in ABF format. A utility program supplied by Axon Instruments converts pClamp 5.5 files to ABF format. Files generated by Axo-Data are not in ABF format.
If the filter cannot read your ABF files, they may have been written by a newer version of pClamp. Check the Bruxton Web site to determine if an update is required.
ABF files can be created by programs designed for high-speed continuous recording, and also by programs designed for pulsed stimulus/response measurements. As a result, the interpretation of an ABF file depends significantly on the recording technique used.
The data in an ABF file is stored as a sequence of episodes. Each episode represents a set of samples recorded continuously. The configuration of episodes in a file depends on the program mode during recording.
If a file is created using a gap-free recording mode, the entire file contains a single episode.
If a file is created using an event-driven mode, the data in the file is stored as a sequence of episodes. The gaps between episodes are not stored. However, since the starting time of each episode is stored, a reader can determine the amount of data discarded in the gaps. Note that if a file is created using event-driven recording with fixed-length episodes, the episodes may overlap in time.
If a file is created using an episodic recording mode, the file is made up of a sequence of episodes. Each episode has the same length. A stimulus may be associated with each episode.
When stimulated acquisition is performed, the stimulus is composed of a sequence of epochs. Each epoch specifies a stimulus amplitude and duration. Each episode is created by stimulating using the entire sequence of epochs, and recording the response.
Although each stimulus is generated using the same sequence of epochs, the stimulus may vary with each episode. For example, the amplitude of one epoch of a stimulus may be incremented each episode.
ABF supports two techniques for varying the parameters of an epoch:
The filter allows the reader to determine what epoch parameters vary with each episode, as well as the actual value of each parameter for each episode.
ABF files contain data from one or more channels. The number of channels acquired is the same throughout a file. Each episode contains data for each channel acquired. For a given episode, the number of samples acquired on each channel is the same.
The sampling interval is specified as the interval between samples on the same channel. For example, if the sampling interval is 50us, successive samples on the same channel are taken at intervals of 50us. The sampling interval used by the a/d converter might be shorter. For example, if the sampling interval is 50us and two channels are being sampled, if a single a/d converter with multiplexer is used, the a/d converter itself will take a sample every 25us.
ABF has an unusual feature that allows two sampling intervals in an episode. The first sampling interval is used for the first part of an episode, and the second sampling rate for the second part. The user defines both sampling intervals, as well as the sample number at which the sampling interval changes. For example, the user can define that an episode contains 2048 samples. The first 1024 samples are to be taken with an interval of 25us and the second 1024 samples with an interval of 100us. The Clampex program of pCLAMP restricts the two sampling intervals to integer multiples of each other. For example, a first interval of 200us and a second interval of 50us are acceptable, while a first interval of 200us and a second interval of 75us are not.
An ABF file can include tags. Each tag is associated with a specific time in the file, and has an associated comment.
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