Scientific data formats

Octave and Matlab filter for loading different scientific file formats are available below. It is the aim that a filter is available for every signal dataformat.

Signal Formats: 8SVX ABF ACQ ADICHT ADPCM AIFC AIFF alpha AMR ASF ATES AVI AVG AVR AXONA BCI2000 BDF BKR BV CDF CEN CFWB CNT CTF DAT DDB DDF DEMG DICOM DIG DDT EBS ecgML EDF EEG EEProbe ESPS FAMOS FEF FIFF FLAC GDF GTF HEA HDF Holter IFF IMA ISHNE KWIK LAB MAT MFER MIDI MIT/BIH MPEG MOV NetCDF NEX NIST NWB OGG OpenXDF Open-Ephys PLX Poly5 PSG QTFF RAW RDF RDT RHD2000 RHS2000 RG64 RMF SCP SEG-2 SEGY SIGIF SMA SMP SND SNDT SPEEX TEAM TDMS TMS32 VOC UFF58unisens WAV WFBD WFT XLS XML
Image Formats (2-D): BMP CDF CPT DCF DIP DICOM DXF EPS EXIF FITS GIF HDF HGT IFS JPEG MNG MPEG NetCDF PS PDF PNG PBMA PBMN PGMA PGMB PNM POLY PPMA PPMB QTFF SVG SXI TIFF WMF XPM
Image Formats (3-D, MESH ): FS# OFF SFM TVF VTK VRML
Matrix Formats: ARFF MAT MM XRFF
Microarray file formats: ATF GAL GPL GPS GPR
Communication Protocol(s): USB
others --- Wikipedia --- FAQS --- BIOSIG-Project

• GDF
  General Data Format for Biosignals
  Software: Biosig toolbox for Matlab/Octave

  Version 3.00 is the latest specification.
  More information and example data is available.

  Features of GDF:
  + GDF combines the advantages of different formats while avoiding the disadvantages.
  + GDF is an open format and has a simple definition.
  + GDF supports different sampling rates, channel specific scaling.
  + GDF supports not only INT16 numbers but also other numeric formats.
  + GDF supports efficient storing of event information.
  + GDF header uses binary data, no rounding errors of the scaling factors.
  + GDF addresses the Y2K issue.
  + GDF enforces overflow detection.
  

  Specification: GDF 1.x
  

  Send your opinion on GDF to me or any other appropriate forum.

• BKR
  EEG Processing Software
  Software: Biosig toolbox for Matlab/Octave

  Definition V2.07: HTML
  Defined by: Department for Medical Informatics University of Technology Graz
  

• Axona DacqUSB
  Axona dacqUSB file format
  Software:

  Specification: AXONA dacqUSB

• EDF, GDF and BDF
  European Data Format for Biosignals and its derivates
  Software: Biosig toolbox for Matlab/Octave

  EDF was defined by a european group of researchers; mainly used for sleep analysis
  GDF supports not only INT16 numbers but also other numeric formats and suggests several improvements to EDF
  BDF was designed by BIOSEMI to support samples with 24bits.
  Specification: EDF GDF BDF

• CNT, EEG, AVG
  Defined by: Neuro Scan
  Specification: C++Header file Neuro Scan format by Paul Bourke, Australia

  Software: Biosig toolbox for Matlab/Octave

  Further software links:
  Conversion tools from the NeuroScan Labs can be found here
  More Matlab tools for NeuroScan can be found here(Jussi T. Virkkala, FI) and here(Arnoud Delorme, FR + USA) and here(Darren L. Weber, AU)

• WFBD, HEA, MIT/BIH
  Defined by: PhysioBank
  Specification Header Signal Annotations ecgcodes.h
  Software: Biosig toolbox for Matlab/Octave Further software: WFDB library subset for Matlab/Octave

• SIGIF:
  SIGnal Interchange Format
  Software: Biosig toolbox for Matlab/Octave

  Specification: Cunha MB; Cunha JP; Oliveira e Silva T. "SIGIF: a digital signal interchange format with application in neurophysiology " IEEE Trans Biomed Eng, 44(5):413-8 1997.

• unisens:
  Unisens - a universal data format
  Software:

• MAT:
  The Matlab dataformat is defined by: The MathWorks
  Specification: The MAT - File Format, Version 5 Copy in EU
  
  g.Tec provides a Matlab-based biomedical data acquisiton system.
  Their Matlab data includes much more information (channel settings etc.) than just the sample numbers.
  
  Software: Biosig toolbox for Matlab/Octave
  This filter was developed to read g.Tec data as well as large Matlab data files from ADInstruments.

• MM (MatrixMarket)
  Specification: MatrixMarket
  Software: Biosig toolbox for Matlab/Octave

• DAT
  Brain Atlas EEG Data File Structure BLSC GMP #820.181-5.2 REVISION: 12/21/90
  loaddat.m V0.35
  Filenames: E*.DAT
  Defined by: BIOLOGIC SYSTEMS CORPORATION

• WFT
  Wave format
  Software: Biosig toolbox for Matlab/Octave
  ??? Gouldis/Nicolet Downloads

  Defined by: Nicolet

• TEAM
  TEAM file format
  Software: Biosig toolbox for Matlab/Octave

  Defined by: Nicolet

• PSG
  GammaTM PSG Software
  loadpsg.m V0.00 <not available>
  Filenames: PatientIDhrminsec.psg
  Defined by: Grass-Astromed

• Alpha-Trace
  defined by B.E.S.T. medical systems
  Software: Biosig toolbox for Matlab/Octave

• ATES Medica / Neurotravel
  defined by ATES Medica Device medical systems
  Software: Biosig toolbox for Matlab/Octave

• Judex
  loadjud.m contributed by Ron Leder
  Defined by: Judex Datasystems

• Vital/FEF
  File Exchange Format for Vital Signs
  Software: Biosig toolbox for Matlab/Octave
  Defined by: CEN/TC251
  Specification: CEN/TS 14271 Public Web site of FEF

• ISO/IEEE 11073
  Health informatics
  Software:
  Defined by: ISO and IEEE
  Specification: Public Web site of IEEE

• SCP
  Standard Communication Protocol - Computer assisted electrocardiography
  Specification: here EN1064:2007 and ISO/DIS 11073/91064 EN 1064:2020
  Defined by: How to implement SCP? more information here
  Software: Biosig toolbox for Matlab/Octave
  Status of implementation: here

• MFER
  Medical waveform Format Encoding Rules
  Defined by: MFER
  Specification: ISO/TS 11073/92001 Biosig toolbox for Matlab/Octave

• DDB / DDF
  Dasylab Data Files
  Defined by: DasyLab
  Specification: Dasylab User Guide (see Chapter 5, pp.171-)

• ecgML
  ECG markup language format
  Specification:
  Reference: H. Wang, F. Azuaje, B. Jung and N. Black. A markup language for electrocardiogram data acquisition and analysis (ecgML) . BMC Medical Informatics and Decision Making 2003, 3:4 This article is available from: here
  

• ISHNE
  ISHNE The ISHNE Holter standard output format
  Specification: ISHNE
  Reference: Zareba W., Locati E. H., Maison Blanche P. The ISHNE holter standard output file format : A step toward compatibility of holter systems Annals of noninvasive electrocardiology (Ann. noninvasive electrocardiol.) 1998, vol. 3 (1), no3, pp. 261-262.
  Remark: acording to Locati (2002) "the ISHNE Holter Format does not require the disclosure of the specific compression and interpolation algorithms ..." this means the format is not an open format.

• Poly5/TMS32
  PortiSystem and Portilab Software
  Specification: Poly5/TMS32

• RDF
  Defined by: Jonathan Hansen at the Hillyard ERP Lab of UCSD
  Specification: ERPSS
  Software: Biosig toolbox for Matlab/Octave

• SMA
  HEM Data Corp.
  Specification: SMA

  Software: Biosig toolbox for Matlab/Octave

• EBS
  EBS Format for Biosignals
  loadebs.m (under construction)
  Specification: http://www.ipb.uni-erlangen.de/ebsspec.html and http://ecco.bsee.swin.edu.au/resres/ebs_spec.html

• HDF
  Hierachical dataformat
  The NCSA HDF Home Page

• NetCDF
  Network common dataformat
  Specification: Unidata
  Software: ncarray (for Octave and Matlab) NetCDF toolbox for Octave NetCDF toolbox for Matlab

• CDF
  Common dataformat
  Specification by National Space Science Data Center

• DIG
  loaddig.m (has to be developed)
  Defined by: Institute for Neurophysiologie

• IFF
  loadiff.m V0.01 (has to be developed)
  Defined by: University of Los Angeles and researches in Australia For more details see ftp://sigftp.cs.tut.fi/pub/eeg-data/standards/iffphys.ps

• RAW
  loadraw.m V1.0 (1st version)
  Best V3.06 Format
  Headerfile : *.rh EEG Data file: *.raw

• RDT
  Internal raw data format
  loadrdt.m V2.01 (well tested)

• RG64
  Raw data format of the Raich 64-channel EEG System
  loadrg64.m V0.20 (under construction)

• XLS
  loadxls.m V1.0 (1st version)
  Extended PC Format Headerfile: *.cnt Datafile: *.eeg, *.xls Defined by: ?

• LabView Data Logger:
  Binary Header File Format
  defined by National Instruments
  labview.m V0.20 (tested and modified by Pierre Bonnard )

• TDMS
  TDMS file format internal structure
  defined by National Instruments
  

• ADICHT and CFWB
  Defined by: ADInstruments
  Specification of ADICHT: not available (ADICHT is a propriatory fileformat) Workaround: save as Matlab format using the Write Matlab (4) Chart Extension.
  Specification of CFWB: a Simple Binary format CFWB for Exporting and Importing of Chart data.

  See also Biosig toolbox for Matlab/Octave

• ACQ
  Defined by: Biopac
  Specification Application Note 156
  Software: Biosig toolbox for Matlab/Octave

• BCI2000
  Defined by: BCI2000
  Specification Project "BCI2000"
  Software: Biosig toolbox for Matlab/Octave

• BrainVision
  Defined by: Brain Products
  Software: Biosig toolbox for Matlab/Octave

• CTF
  Defined by: CTF Systems Inc.
  Software: Biosig toolbox for Matlab/Octave

• DEMG
  Defined by: DelSys Inc.
  Software: Biosig toolbox for Matlab/Octave

• EEProbe
  Defined by: ANT
  Specification: not available (proprietary format)
  Software: Robert Oostenveld's MEX-files work well with
  Biosig toolbox for Matlab/Octave

• FIFF
  Defined by: Neuromag (?)
  Specification: not available (proprietary format)
  Software: Neuromag FIFF-file access functions for Matlab work well with
  Biosig toolbox for Matlab/Octave

• GTF
  Defined by: EBNeuro
  Specification: not available
  Software: Biosig toolbox for Matlab/Octave

• NEX
  Defined by: Neuroexplorer
  Specification:
  Software: Biosig toolbox for Matlab/Octave

• KWIK
  Defined by: Open-Ephys
  Specification:
  Software: OpenEPhys

• OpenEPhys
  Defined by: Open-EPhys
  Specification:
  Software: https://github.com/NeurodataWithoutBorders

• NWB
  Defined by: Neurodata Without Borders
  Specification:
  Software: https://github.com/NeurodataWithoutBorders

• OpenXDF
  Defined by: Neurotronics, Inc.
  Specification: OpenXDF
  Software:

• PLX
  Defined by: Plexon Inc.
  Specification:
  Software: Biosig toolbox for Matlab/Octave

• RHD2000
  Defined by: IntanTech
  Specification
  Software:

• RHS2000
  Defined by: IntanTech
  Specification
  Software:

• DDT
  Defined by: Plexon Inc.
  Specification:
  Software: Biosig toolbox for Matlab/Octave

• AIFF and AIFC
  Specification: here or here or here
  Format: Audio Interchange File Format
  Software: Biosig toolbox for Matlab/Octave

• AMR
  Specification: ???
  Format: Adaptive Multi-Rate Format
  Software: ???

• IMA ADPCM
  Specification: here
  Format: Adaptive Differential Pulse Code Modulation

  Defined by:International Multimedia Association (IMA)
  Software:

• ASF
  Specification: Microsoft
  Format: Advanced System Format (*.ASF)
  Software: you may start with ASFOPEN.M Ver 0.10

• FLAC
  Specification: here
  Format: Free Lossless Audio Codec
  Software: Download

• FAMOS
  Specification: ASCII header and binary data
  Format:FAMOS
  Software: http://www.imc-berlin.de

• SND
  Specification: here
  Format: Next/SUN sound file (*.AU)
  Software: Biosig toolbox for Matlab/Octave

• 8SVX
  Specification: IFF/8SVX
  Software: SoX - Sound Exchange Library

• AVR
  Specification: AVR
  Software: SoX - Sound Exchange Library

• ESPS NIST SMP SNDT
  Specification: Description by SoX
  Software: SoX - Sound Exchange Library

• SPEEX
  Specification: Manual
  Software: Download

• VOC
  Specification: VOC
  Software: SoX - Sound Exchange Library

• WAV
  Specification: here or here
  Format: Microsofts PCM data format
  Software: Biosig toolbox for Matlab/Octave

• UFF58
  Specification:
  UFF
  UFF58
  UFF58b

• MIDI
  Defined by: MIDI Manufactures Association
  Specification: (i) The MIDI File Format (ii) Standard MIDI File (SMF) Format
  Software: (i) MIDI toolbox (ii) Audio-to-Midi converter (iii) MIDI and Matlab

• MPEG
  Specification: here
  Software: MPEG4IP

• OGG
  Specification: here
  here
  Vorbis
  Xiph
  Software: ???

• SEG-2, SEGY:
  A seismic (radar) data format
  Defined by: DeTeC - Demining Technology Center
  Specification: Pullan S.E. 1990 Recommended standard for seismic (/radar) files in the personal computer environment: Geophysics: 55, no 09, 1260-1271.

• AVI - Audio Video Interleave format
  Specification: here or here
  Format: Audio Video Interleave Format
  
  Software: Biosig toolbox for Matlab/Octave

• MOV/QTFF Apple Quicktime format
  Specification: Apple QuickTime File Format
  
  Software: Biosig toolbox for Matlab/Octave

• ABF
  Format: Axon Binary Format
  Specification: pCLAMP and AxoScope File Support
  Software: Biosig toolbox for Matlab/Octave

• ATF, GAL, GPL, GPR, GPS,
  Format: Axon Text Format
  Specification:GenePix File Formats
  Software: Biosig toolbox for Matlab/Octave

• BMP/DIB
  Specification:
  Format: Bitmap image format, device independant bitmat
  Software: Biosig toolbox for Matlab/Octave

• DICOM:
  Specification: The DICOM Standard status
  The DICOM Standard status
  Software: Overview and
  Biosig toolbox for Matlab/Octave

• DXF: AutoCad file exchange format
  Specification:
  AutoCad 2004
  AutoCad 2002
  AutoCad 2000
  AutoCad 14
  

• FITS: Flexible Image Transport format
  Specification
  Format: Standard data format for astronomy
  Software: FITS Viewer
  Biosig toolbox for Matlab/Octave

• HGT:
  Specification
  Format:
  Software:
  Biosig toolbox for Matlab/Octave

• JPEG
  Specification:
  Independent JPEG Group
  JPEG Consortium
  Format: Joint Photographic Experts Group
  Software:
  Independent JPEG Group

• PNG
  Specification: PNG
  Format: Portable Network Graphics
  Software: Biosig toolbox for Matlab/Octave

• FS3, FS4: FreeServer Surface File Formats
  Description
  Biosig toolbox for Matlab/Octave

• IFS
  Examples
  Format: Image data format: Medical/Heart/Coronary Artery Ultrasound
  

• PNM (PBMA, PGMA, PPMA, PBMB, PGMB, PPMB)
  Specification: NETPBM
  Biosig toolbox for Matlab/Octave

• SXI
  Specification
  Format: data format for Ultrasound data
  

• SVG: Scalable Vector Graphics
  Defined by: W3C World Wide Web Consortion (W3C)
  Specification: World Wide Web Consortion (W3C)

• EXIF: Exchangeable Image File Formats for digital still cameras
  Specification: DCF, EXIF

• TIFF: Tagged Image File Format
  Defined by: Aldus Developer's Association which has merged with Adobe.
  Specification: TIFF @ Adobe
  TIFF6
  The Unofficial TIFF homepage

• TVF: Triangel Vertex file format
  Defined by: ???
  Specification: TVF

• VTK: Visualization toolkit
  Defined by: VTK
  Specification: VTK format 4.2

• XML FDA:
  Defined by: The Digital ECG Data Submissions at FDA
  Specification: FDA XML Dataformat Specification

• USB
  Defined by: USB consortium
  Specification: USB 2.0 Specification
  Software: USB Snoopy

• ARFF,XRFF
  Defined by: WEKA

Other Data Formats

• ASTM- E - 1467: Standard Specification for Transferring Digital Neurophysiological Data Between Independent Computer Systems ASTM

• Audio data formats:
  Audio File Library
  libsndfile

• PDP Other Data Formats (by Paul Bourke, Australia)

• HL7aECG

• HL7

• Raw Digital Photo Decoding

• Neuroimaging volume data file formats

• Formats supported by libRASCH

• Seismic (radar) data format: Technical Standards of the Society of Exploration Geophysicist