Bio-Formats Documentation Release 5.0.8 The Open Microscopy Environment February 07, 2015 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 26 5 Using Bio-Formats with ImageJ and Fiji 27 5.1 ImageJ overview ................................................... 27 5.2 Fiji overview ..................................................... 28 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 28 5.4 Installing Bio-Formats in ImageJ .......................................... 29 5.5 Using Bio-Formats to load images into ImageJ ................................... 31 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 34 6 Command line tools 38 6.1 Command line tools introduction .......................................... 38 6.2 Displaying images and metadata ........................................... 39 6.3 Converting a file to different format ......................................... 40 6.4 Validating XML in an OME-TIFF .......................................... 41 6.5 Editing XML in an OME-TIFF ........................................... 42 7 OMERO 43 8 Image server applications 44 8.1 BISQUE ....................................................... 44 8.2 OME Server ..................................................... 44 9 Libraries and scripting applications 47 9.1 FARSIGHT ...................................................... 47 9.2 i3dcore ........................................................ 47 9.3 ImgLib ........................................................ 47 9.4 ITK .......................................................... 48 9.5 Qu for MATLAB ................................................... 48 9.6 Subimager ...................................................... 48 10 Numerical data processing applications 49 10.1 IDL .......................................................... 49 10.2 KNIME ........................................................ 49 10.3 MATLAB ...................................................... 49 10.4 VisAD ........................................................ 50 i 11 Visualization and analysis applications 51 11.1 Bitplane Imaris .................................................... 51 11.2 CellProfiler ...................................................... 51 11.3 Comstat2 ....................................................... 52 11.4 Endrov ........................................................ 52 11.5 FocalPoint ...................................................... 52 11.6 Graphic Converter .................................................. 52 11.7 Icy .......................................................... 53 11.8 imago ......................................................... 53 11.9 Iqm .......................................................... 53 11.10 Macnification ..................................................... 53 11.11 MIPAV ........................................................ 53 11.12 Vaa3D ........................................................ 54 11.13 VisBio ........................................................ 54 11.14 XuvTools ....................................................... 55 III Developer Documentation 56 12 Using Bio-Formats 57 12.1 An in-depth guide to using Bio-Formats ....................................... 57 12.2 Obtaining and building Bio-Formats ......................................... 59 12.3 Generating test images ................................................ 61 13 Bio-Formats as a Java library 63 13.1 API documentation .................................................. 63 13.2 Examples ....................................................... 64 14 Interfacing from non-Java code 75 14.1 Interfacing with Bio-Formats from non-Java code .................................. 75 14.2 Bio-Formats C++ bindings .............................................. 75 14.3 Build instructions for C++ bindings ......................................... 75 14.4 Building C++ bindings in Windows ......................................... 77 14.5 Building C++ bindings in Mac OS X ........................................ 78 14.6 Building C++ bindings in Linux ........................................... 79 15 Writing new Bio-Formats file format readers 80 15.1 Bio-Formats file format reader guide ........................................ 80 16 Contributing to Bio-Formats 84 16.1 Testing individual commits (internal developers) .................................. 84 16.2 Public test data .................................................... 85 16.3 Bio-Formats service and dependency infrastructure ................................. 88 16.4 Code generation with xsd-fu ............................................. 90 IV Formats 92 17 Dataset Structure Table 94 17.1 Flex Support ..................................................... 97 18 Supported Formats 98 18.1 3i SlideBook ..................................................... 103 18.2 Andor Bio-Imaging Division (ABD) TIFF ..................................... 104 18.3 AIM ......................................................... 104 18.4 Alicona 3D ...................................................... 105 18.5 Amersham Biosciences Gel ............................................. 106 18.6 Amira Mesh ..................................................... 107 18.7 Analyze 7.5 ...................................................... 107 18.8 Animated PNG .................................................... 108 18.9 Aperio AFI ...................................................... 109 18.10 Aperio SVS TIFF ................................................... 109 ii 18.11 Applied Precision CellWorX ............................................. 110 18.12 AVI (Audio Video Interleave) ............................................ 111 18.13 Axon Raw Format .................................................. 112 18.14 BD Pathway ..................................................... 112 18.15 Becker & Hickl SPCImage .............................................. 113 18.16 Bio-Rad Gel ..................................................... 114 18.17 Bio-Rad PIC ..................................................... 114 18.18 Bio-Rad SCN ..................................................... 115 18.19 Bitplane Imaris .................................................... 116 18.20 Bruker MRI ..................................................... 117 18.21 Burleigh ....................................................... 117 18.22 Canon DNG ..................................................... 118 18.23 Cellomics ....................................................... 119 18.24 cellSens VSI ..................................................... 120 18.25 CellVoyager ..................................................... 120 18.26 DeltaVision ...................................................... 121 18.27 DICOM ........................................................ 122 18.28 ECAT7 ........................................................ 123 18.29 EPS (Encapsulated PostScript) ............................................ 123 18.30 Evotec/PerkinElmer Opera Flex ........................................... 124 18.31 FEI .......................................................... 125 18.32 FEI TIFF ....................................................... 126 18.33 FITS (Flexible Image Transport System) ...................................... 126 18.34 Gatan Digital Micrograph .............................................. 127 18.35 Gatan Digital Micrograph 2 ............................................. 128 18.36 GIF (Graphics Interchange Format) ......................................... 128 18.37 Hamamatsu Aquacosmos NAF ............................................ 129 18.38 Hamamatsu HIS ................................................... 130 18.39 Hamamatsu ndpi ................................................... 130 18.40 Hamamatsu VMS .................................................. 131 18.41 Hitachi S-4800 .................................................... 132 18.42 ICS (Image Cytometry Standard) .......................................... 133 18.43 Imacon ........................................................ 133 18.44 ImagePro Sequence ................................................. 134 18.45 ImagePro Workspace ................................................. 135 18.46 IMAGIC ....................................................... 136 18.47 IMOD ........................................................ 136 18.48 Improvision Openlab LIFF .............................................. 137 18.49 Improvision Openlab Raw .............................................. 138 18.50 Improvision TIFF .................................................. 139 18.51 Imspector OBF .................................................... 139 18.52 InCell 1000 ...................................................... 140 18.53 InCell 3000 ...................................................... 141 18.54 INR .......................................................... 141 18.55 Inveon ........................................................ 142 18.56 IPLab ......................................................... 142 18.57 IPLab-Mac ...................................................... 143 18.58