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Bio-Formats Documentation Release 5.0.4 Bio-Formats Documentation Release 5.0.4 The Open Microscopy Environment September 01, 2014 CONTENTS I About Bio-Formats 2 1 Why Java? 4 2 Bio-Formats metadata processing 5 3 Help 6 3.1 Reporting a bug ................................................... 6 3.2 Troubleshooting ................................................... 7 4 Bio-Formats versions 9 4.1 Version history .................................................... 9 II User Information 25 5 Using Bio-Formats with ImageJ and Fiji 26 5.1 ImageJ overview ................................................... 26 5.2 Fiji overview ..................................................... 27 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 27 5.4 Installing Bio-Formats in ImageJ .......................................... 28 5.5 Using Bio-Formats to load images into ImageJ ................................... 30 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 33 6 Command line tools 37 6.1 Command line tools introduction .......................................... 37 6.2 Displaying images and metadata ........................................... 38 6.3 Converting a file to different format ......................................... 39 6.4 Validating XML in an OME-TIFF .......................................... 40 6.5 Editing XML in an OME-TIFF ........................................... 41 7 OMERO 42 8 Image server applications 43 8.1 BISQUE ....................................................... 43 8.2 OME Server ..................................................... 43 9 Libraries and scripting applications 46 9.1 FARSIGHT ...................................................... 46 9.2 i3dcore ........................................................ 46 9.3 ImgLib ........................................................ 46 9.4 ITK .......................................................... 47 9.5 Qu for MATLAB ................................................... 47 9.6 Subimager ...................................................... 47 10 Numerical data processing applications 48 10.1 IDL .......................................................... 48 10.2 KNIME ........................................................ 48 10.3 MATLAB ...................................................... 48 10.4 VisAD ........................................................ 49 i 11 Visualization and analysis applications 50 11.1 Bitplane Imaris .................................................... 50 11.2 CellProfiler ...................................................... 50 11.3 Comstat2 ....................................................... 51 11.4 Endrov ........................................................ 51 11.5 FocalPoint ...................................................... 51 11.6 Graphic Converter .................................................. 51 11.7 Icy .......................................................... 52 11.8 imago ......................................................... 52 11.9 Iqm .......................................................... 52 11.10 Macnification ..................................................... 52 11.11 MIPAV ........................................................ 52 11.12 Vaa3D ........................................................ 53 11.13 VisBio ........................................................ 53 11.14 XuvTools ....................................................... 54 III Developer Documentation 55 12 Using Bio-Formats 56 12.1 An in-depth guide to using Bio-Formats ....................................... 56 12.2 Obtaining and building Bio-Formats ......................................... 58 12.3 Generating test images ................................................ 60 13 Bio-Formats as a Java library 62 13.1 API documentation .................................................. 62 13.2 Examples ....................................................... 63 14 Interfacing from non-Java code 73 14.1 Interfacing with Bio-Formats from non-Java code .................................. 73 14.2 Bio-Formats C++ bindings .............................................. 73 14.3 Build instructions for C++ bindings ......................................... 73 14.4 Building C++ bindings in Windows ......................................... 75 14.5 Building C++ bindings in Mac OS X ........................................ 76 14.6 Building C++ bindings in Linux ........................................... 77 15 Writing new Bio-Formats file format readers 78 15.1 Bio-Formats file format reader guide ........................................ 78 16 Contributing to Bio-Formats 82 16.1 Testing individual commits (internal developers) .................................. 82 16.2 Public test data .................................................... 83 16.3 Bio-Formats service and dependency infrastructure ................................. 86 16.4 Code generation with xsd-fu ............................................. 88 IV Formats 90 17 Dataset Structure Table 92 17.1 Flex Support ..................................................... 95 18 Supported Formats 96 18.1 3i SlideBook ..................................................... 101 18.2 Andor Bio-Imaging Division (ABD) TIFF ..................................... 102 18.3 AIM ......................................................... 102 18.4 Alicona 3D ...................................................... 103 18.5 Amersham Biosciences Gel ............................................. 104 18.6 Amira Mesh ..................................................... 105 18.7 Analyze 7.5 ...................................................... 105 18.8 Animated PNG .................................................... 106 18.9 Aperio AFI ...................................................... 107 18.10 Aperio SVS TIFF ................................................... 107 ii 18.11 Applied Precision CellWorX ............................................. 108 18.12 AVI (Audio Video Interleave) ............................................ 109 18.13 Axon Raw Format .................................................. 110 18.14 BD Pathway ..................................................... 110 18.15 Becker & Hickl SPCImage .............................................. 111 18.16 Bio-Rad Gel ..................................................... 112 18.17 Bio-Rad PIC ..................................................... 112 18.18 Bio-Rad SCN ..................................................... 113 18.19 Bitplane Imaris .................................................... 114 18.20 Bruker MRI ..................................................... 115 18.21 Burleigh ....................................................... 115 18.22 Canon DNG ..................................................... 116 18.23 Cellomics ....................................................... 117 18.24 cellSens VSI ..................................................... 118 18.25 CellVoyager ..................................................... 118 18.26 DeltaVision ...................................................... 119 18.27 DICOM ........................................................ 120 18.28 ECAT7 ........................................................ 121 18.29 EPS (Encapsulated PostScript) ............................................ 121 18.30 Evotec/PerkinElmer Opera Flex ........................................... 122 18.31 FEI .......................................................... 123 18.32 FEI TIFF ....................................................... 124 18.33 FITS (Flexible Image Transport System) ...................................... 124 18.34 Gatan Digital Micrograph .............................................. 125 18.35 Gatan Digital Micrograph 2 ............................................. 126 18.36 GIF (Graphics Interchange Format) ......................................... 126 18.37 Hamamatsu Aquacosmos NAF ............................................ 127 18.38 Hamamatsu HIS ................................................... 128 18.39 Hamamatsu ndpi ................................................... 128 18.40 Hamamatsu VMS .................................................. 129 18.41 Hitachi S-4800 .................................................... 130 18.42 ICS (Image Cytometry Standard) .......................................... 131 18.43 Imacon ........................................................ 131 18.44 ImagePro Sequence ................................................. 132 18.45 ImagePro Workspace ................................................. 133 18.46 IMAGIC ....................................................... 134 18.47 IMOD ........................................................ 134 18.48 Improvision Openlab LIFF .............................................. 135 18.49 Improvision Openlab Raw .............................................. 136 18.50 Improvision TIFF .................................................. 137 18.51 Imspector OBF .................................................... 137 18.52 InCell 1000 ...................................................... 138 18.53 InCell 3000 ...................................................... 139 18.54 INR .......................................................... 139 18.55 Inveon ........................................................ 140 18.56 IPLab ......................................................... 140 18.57 IPLab-Mac ...................................................... 141 18.58
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